diff --git a/xls/build_rules/tests/BUILD b/xls/build_rules/tests/BUILD
index 94d0395eea..7e47ce1059 100644
--- a/xls/build_rules/tests/BUILD
+++ b/xls/build_rules/tests/BUILD
@@ -296,6 +296,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "add_one_dslx_ir",
     dslx_top = "main",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":add_one_dslx",
 )
 
diff --git a/xls/dslx/ir_convert/ir_converter_main.cc b/xls/dslx/ir_convert/ir_converter_main.cc
index 0b933cf3a1..908a1afbfc 100644
--- a/xls/dslx/ir_convert/ir_converter_main.cc
+++ b/xls/dslx/ir_convert/ir_converter_main.cc
@@ -101,7 +101,9 @@ absl::Status RealMain(absl::Span<const std::string_view> paths) {
   bool warnings_as_errors = ir_converter_options.warnings_as_errors();
   bool type_inference_v2 = ir_converter_options.type_inference_v2();
   bool lower_to_proc_scoped_channels =
-      ir_converter_options.lower_to_proc_scoped_channels();
+      ir_converter_options.has_lower_to_proc_scoped_channels()
+          ? ir_converter_options.lower_to_proc_scoped_channels()
+          : false;
   bool force_implicit_token_calling_convention =
       ir_converter_options.force_implicit_token_calling_convention();
   bool emit_trace = ir_converter_options.emit_trace();
diff --git a/xls/dslx/ir_convert/ir_converter_options_flags.cc b/xls/dslx/ir_convert/ir_converter_options_flags.cc
index 07b9e801ad..192473a706 100644
--- a/xls/dslx/ir_convert/ir_converter_options_flags.cc
+++ b/xls/dslx/ir_convert/ir_converter_options_flags.cc
@@ -112,6 +112,13 @@ absl::StatusOr<bool> SetOptionsFromFlags(IrConverterOptionsFlagsProto& proto) {
     any_flags_set |= FLAGS_##__x.IsSpecifiedOnCommandLine(); \
     proto.set_##__x(absl::GetFlag(FLAGS_##__x));             \
   }
+#define POPULATE_FLAG_IF_SPECIFIED(__x)            \
+  {                                                \
+    if (FLAGS_##__x.IsSpecifiedOnCommandLine()) {  \
+      any_flags_set = true;                        \
+      proto.set_##__x(absl::GetFlag(FLAGS_##__x)); \
+    }                                              \
+  }
 #define POPULATE_OPTIONAL_FLAG(__x)                          \
   {                                                          \
     any_flags_set |= FLAGS_##__x.IsSpecifiedOnCommandLine(); \
@@ -143,7 +150,7 @@ absl::StatusOr<bool> SetOptionsFromFlags(IrConverterOptionsFlagsProto& proto) {
   POPULATE_OPTIONAL_FLAG(interface_proto_file);
   POPULATE_OPTIONAL_FLAG(interface_textproto_file);
   POPULATE_FLAG(type_inference_v2);
-  POPULATE_FLAG(lower_to_proc_scoped_channels);
+  POPULATE_FLAG_IF_SPECIFIED(lower_to_proc_scoped_channels);
   POPULATE_FLAG(force_implicit_token_calling_convention);
   POPULATE_REPEATED_FLAG(configured_values);
   POPULATE_FLAG(emit_assert);
diff --git a/xls/dslx/tests/trace_fmt_array/BUILD b/xls/dslx/tests/trace_fmt_array/BUILD
index a1b426a126..0a197ddaa5 100644
--- a/xls/dslx/tests/trace_fmt_array/BUILD
+++ b/xls/dslx/tests/trace_fmt_array/BUILD
@@ -34,6 +34,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "test_target",
     dslx_top = "traceit",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":test_target_library",
 )
 
diff --git a/xls/examples/BUILD b/xls/examples/BUILD
index a8a524bf7a..b981c8cf20 100644
--- a/xls/examples/BUILD
+++ b/xls/examples/BUILD
@@ -961,9 +961,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "delay_loopback_channel_ir",
     dslx_top = "Delay",
-    ir_conv_args = {
-        "lower_to_proc_scoped_channels": "true",
-    },
+    ir_conv_args = {"lower_to_proc_scoped_channels": "true"},
     ir_file = "delay_loopback_channel.ir",
     library = ":delay_loopback_channel_dslx",
 )
@@ -1048,6 +1046,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "constraint_ir",
     dslx_top = "main",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "constraint.ir",
     library = ":constraint_dslx",
 )
@@ -1242,6 +1241,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "serialized_decomposer_ir",
     dslx_top = "serialized_decomposer",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "serialized_decomposer.ir",
     library = ":serialized_decomposer_dslx",
 )
@@ -1391,9 +1391,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "proc_network_ir",
     dslx_top = "Initiator",
-    ir_conv_args = {
-        "lower_to_proc_scoped_channels": "false",
-    },
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "proc_network.ir",
     library = ":proc_network_dslx",
 )
@@ -1401,9 +1399,7 @@ xls_dslx_ir(
 xls_dslx_ir(
     name = "proc_network_proc_scoped_ir",
     dslx_top = "Initiator",
-    ir_conv_args = {
-        "lower_to_proc_scoped_channels": "true",
-    },
+    ir_conv_args = {"lower_to_proc_scoped_channels": "true"},
     ir_file = "proc_network_proc_scoped.ir",
     library = ":proc_network_dslx",
 )
diff --git a/xls/examples/assertions/BUILD b/xls/examples/assertions/BUILD
index f1a26d67df..84fdec0445 100644
--- a/xls/examples/assertions/BUILD
+++ b/xls/examples/assertions/BUILD
@@ -48,6 +48,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "assertions_ir",
     dslx_top = "main",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "assertions.ir",
     library = ":assertions_dslx",
 )
diff --git a/xls/examples/dslx_module/BUILD b/xls/examples/dslx_module/BUILD
index 94575d3a5b..8f3983baea 100644
--- a/xls/examples/dslx_module/BUILD
+++ b/xls/examples/dslx_module/BUILD
@@ -65,6 +65,7 @@ xls_dslx_ir(
     name = "some_caps_streaming_configured_ir",
     dslx_top = "some_caps_specialized",
     ir_conv_args = {
+        "lower_to_proc_scoped_channels": "false",
         # Set fifo config for multi-proc codegen.
         # It needs to know what configuration to use for the fifo.
         "default_fifo_config": "depth: 4, bypass: true, " +
@@ -91,6 +92,7 @@ xls_dslx_opt_ir(
     # liveness instead of spawn tree. This is done to avoid having to deal with mangled names.
     dslx_top = "manual_chan_caps_specialized",
     ir_conv_args = {
+        "lower_to_proc_scoped_channels": "false",
         # Set fifo config for multi-proc codegen.
         # It needs to know what configuration to use for the fifo.
         "default_fifo_config": "depth: 4, bypass: true, " +
diff --git a/xls/examples/parameterized/BUILD b/xls/examples/parameterized/BUILD
index 647a872376..e7e4f250bc 100644
--- a/xls/examples/parameterized/BUILD
+++ b/xls/examples/parameterized/BUILD
@@ -62,6 +62,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "design_ir",
     dslx_top = "design_top",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "design.ir",
     library = "design_lib",
 )
diff --git a/xls/examples/protobuf/BUILD b/xls/examples/protobuf/BUILD
index 0bd5911861..32686751ce 100644
--- a/xls/examples/protobuf/BUILD
+++ b/xls/examples/protobuf/BUILD
@@ -47,6 +47,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "verint_encode_ir",
     dslx_top = "varint_encode_u32",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "varint_encode.ir",
     library = ":varint_encode_dslx",
 )
diff --git a/xls/jit/BUILD b/xls/jit/BUILD
index f5fd376d3a..7b760ec872 100644
--- a/xls/jit/BUILD
+++ b/xls/jit/BUILD
@@ -1217,6 +1217,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "multi_function",
     dslx_top = "multi_function_one",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":multi_function_dslx",
 )
 
@@ -1285,6 +1286,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "multi_function_with_trace",
     dslx_top = "multi_function_one",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":multi_function_with_trace_dslx",
 )
 
diff --git a/xls/jit/testdata/v1/BUILD b/xls/jit/testdata/v1/BUILD
index 46c6932abb..a18e14329b 100644
--- a/xls/jit/testdata/v1/BUILD
+++ b/xls/jit/testdata/v1/BUILD
@@ -28,12 +28,14 @@ xls_dslx_ir(
     name = "test_ir",
     srcs = ["test.x"],
     dslx_top = "main",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
 )
 
 xls_dslx_ir(
     name = "multi_proc_ir",
     srcs = ["multi_proc.x"],
     dslx_top = "proc_ten",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
 )
 
 xls_dslx_ir(
diff --git a/xls/jit/testdata/v2/BUILD b/xls/jit/testdata/v2/BUILD
index dc9b79801e..13957074d6 100644
--- a/xls/jit/testdata/v2/BUILD
+++ b/xls/jit/testdata/v2/BUILD
@@ -28,12 +28,14 @@ xls_dslx_ir(
     name = "test_ir",
     srcs = ["test.x"],
     dslx_top = "main",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
 )
 
 xls_dslx_ir(
     name = "multi_proc_ir",
     srcs = ["multi_proc.x"],
     dslx_top = "proc_ten",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
 )
 
 xls_dslx_ir(
diff --git a/xls/modules/aes/BUILD b/xls/modules/aes/BUILD
index 5978ce89bd..2ecb33473c 100644
--- a/xls/modules/aes/BUILD
+++ b/xls/modules/aes/BUILD
@@ -69,6 +69,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "aes_ctr",
     dslx_top = "aes_ctr",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":aes_ctr_dslx",
 )
 
@@ -112,6 +113,7 @@ cc_test(
 xls_dslx_ir(
     name = "aes_decrypt",
     dslx_top = "decrypt",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":aes_dslx",
 )
 
@@ -133,6 +135,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "aes_encrypt",
     dslx_top = "encrypt",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":aes_dslx",
 )
 
@@ -165,6 +168,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "aes_gcm",
     dslx_top = "aes_gcm",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":aes_gcm_dslx",
 )
 
@@ -231,6 +235,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "aes_ghash",
     dslx_top = "ghash",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":ghash_dslx",
 )
 
diff --git a/xls/modules/rle/BUILD b/xls/modules/rle/BUILD
index bc76c22b8a..52ab42014e 100644
--- a/xls/modules/rle/BUILD
+++ b/xls/modules/rle/BUILD
@@ -131,6 +131,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "rle_enc_ir",
     dslx_top = "RunLengthEncoder32",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "rle_enc.ir",
     library = "rle_enc_dslx",
 )
@@ -258,6 +259,7 @@ xls_dslx_test(
 xls_dslx_ir(
     name = "rle_dec_ir",
     dslx_top = "RunLengthDecoder32",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     ir_file = "rle_dec.ir",
     library = "rle_dec_dslx",
 )
diff --git a/xls/tools/testdata/BUILD b/xls/tools/testdata/BUILD
index 4b2d31d78d..f6b126b2df 100644
--- a/xls/tools/testdata/BUILD
+++ b/xls/tools/testdata/BUILD
@@ -82,6 +82,7 @@ xls_dslx_ir(
 xls_dslx_ir(
     name = "eval_proc_main_test_ir",
     dslx_top = "test_proc",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":eval_proc_main_test",
 )
 
@@ -166,6 +167,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "eval_proc_main_zero_size_test_ir",
     dslx_top = "test_proc",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":eval_proc_main_zero_size_test",
 )
 
@@ -246,6 +248,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "eval_proc_main_conditional_test_ir",
     dslx_top = "test_proc",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":eval_proc_main_conditional_test",
 )
 
@@ -339,6 +342,7 @@ xls_dslx_library(
 xls_dslx_ir(
     name = "eval_proc_main_test_memory",
     dslx_top = "test_proc",
+    ir_conv_args = {"lower_to_proc_scoped_channels": "false"},
     library = ":eval_proc_main_test_memory_lib",
 )