diff --git a/rojo-test/syncback-test-snapshots/end_to_end__rojo_test__syncback_util__nested_projects_weird-stdout.snap b/rojo-test/syncback-test-snapshots/end_to_end__rojo_test__syncback_util__nested_projects_weird-stdout.snap
index 370ed871..b727e039 100644
--- a/rojo-test/syncback-test-snapshots/end_to_end__rojo_test__syncback_util__nested_projects_weird-stdout.snap
+++ b/rojo-test/syncback-test-snapshots/end_to_end__rojo_test__syncback_util__nested_projects_weird-stdout.snap
@@ -4,5 +4,3 @@ expression: normalized_stdout
 ---
 Writing src/modules/ClientModule.luau
 Writing src/modules/ServerModule.luau
-Removing client-only.project.json5
-Removing server-only.project.json5
diff --git a/src/syncback/mod.rs b/src/syncback/mod.rs
index e391c23b..be41b797 100644
--- a/src/syncback/mod.rs
+++ b/src/syncback/mod.rs
@@ -418,6 +418,14 @@ pub fn syncback_loop_with_stats(
                 log::debug!("Skipping project file: {}", old_path.display());
                 continue;
             }
+            // Never remove any nested project files - they define project structure
+            // and may be referenced via $path from other project files
+            if let Some(file_name) = old_path_norm.file_name().and_then(|n| n.to_str()) {
+                if file_name.ends_with(".project.json5") || file_name.ends_with(".project.json") {
+                    log::debug!("Skipping nested project file: {}", old_path.display());
+                    continue;
+                }
+            }
             // Skip if this exact path is being written to
             if added_paths.contains(&old_path_norm) {
                 continue;