diff --git a/platform/build-scripts/product-dsl/src/xml/XmlDependencyUpdater.kt b/platform/build-scripts/product-dsl/src/xml/XmlDependencyUpdater.kt
index 27456aee82d2..09298cc7f76b 100644
--- a/platform/build-scripts/product-dsl/src/xml/XmlDependencyUpdater.kt
+++ b/platform/build-scripts/product-dsl/src/xml/XmlDependencyUpdater.kt
@@ -21,6 +21,18 @@ private const val REGION_MARKER = "region Generated dependencies"
 // Legacy marker for backward compatibility with existing files
 private const val LEGACY_MARKER = "editor-fold desc=\"Generated dependencies"
 
+/**
+ * Returns true when the comment is one of the fold/region markers owned by the generator
+ * (region start/end or legacy editor-fold start/end). Such comments must not be treated as
+ * user-authored content to preserve when rewriting the `<dependencies>` section.
+ */
+private fun isFoldMarkerComment(commentText: String): Boolean {
+  return commentText.contains(REGION_MARKER) ||
+         commentText.contains(LEGACY_MARKER) ||
+         commentText.contains("endregion") ||
+         commentText.contains("end editor-fold")
+}
+
 private enum class RegionType { NONE, WRAPS_ENTIRE_SECTION, INSIDE_SECTION }
 
 private data class RemovalRange(
@@ -31,6 +43,7 @@ private data class RemovalRange(
 private sealed class DepEntry {
   data class Plugin(val id: String) : DepEntry()
   data class Module(val name: String) : DepEntry()
+  data class Comment(val text: String) : DepEntry()
 }
 
 private data class DepOccurrence(
@@ -180,6 +193,7 @@ internal fun buildUpdatedXmlDependenciesContent(
     when (val entry = occurrence.entry) {
       is DepEntry.Plugin -> preserveExistingPlugin?.invoke(entry.id) == true
       is DepEntry.Module -> preserveExistingModule?.invoke(entry.name) == true
+      is DepEntry.Comment -> true
     }
   }
 
@@ -335,6 +349,20 @@ private fun parseDependenciesInfo(content: String, allowInsideSectionRegion: Boo
             }
           }
         }
+        XMLStreamConstants.COMMENT -> if (depth > 0) {
+          val locOffset = reader.location.characterOffset
+          val startOffset = content.lastIndexOf("<!--", locOffset)
+          if (startOffset >= 0) {
+            val endIdx = content.indexOf("-->", startOffset)
+            if (endIdx >= 0) {
+              val fullText = content.substring(startOffset, endIdx + "-->".length)
+              if (!isFoldMarkerComment(fullText)) {
+                entries.add(DepEntry.Comment(fullText))
+                entryOffsets.add(startOffset)
+              }
+            }
+          }
+        }
         XMLStreamConstants.END_ELEMENT -> if (depth > 0) {
           depth--
           if (depth == 0) {
@@ -428,6 +456,7 @@ private fun dedupeOccurrencesKeepingFirst(
       is DepEntry.Plugin -> {
         if (entry.id in generatedPluginIds || !seenPlugins.add(entry.id)) continue
       }
+      is DepEntry.Comment -> Unit
     }
     result.add(entry)
   }
@@ -447,6 +476,7 @@ private fun collectDuplicateRemovalRanges(
     val shouldRemove = when (val entry = occurrence.entry) {
       is DepEntry.Module -> entry.name in generatedModuleNames || !seenModules.add(entry.name)
       is DepEntry.Plugin -> entry.id in generatedPluginIds || !seenPlugins.add(entry.id)
+      is DepEntry.Comment -> false
     }
     if (shouldRemove) {
       createEntryRemovalRange(content, occurrence)?.let(ranges::add)
@@ -459,6 +489,7 @@ private fun createEntryRemovalRange(content: String, occurrence: DepOccurrence):
   val tagName = when (occurrence.entry) {
     is DepEntry.Module -> "module"
     is DepEntry.Plugin -> "plugin"
+    is DepEntry.Comment -> return null
   }
   val startOffset = occurrence.startOffset
   if (startOffset < 0) return null
@@ -621,6 +652,7 @@ private fun buildWithEntries(indent: String, manualEntries: List<DepEntry>, auto
       when (entry) {
         is DepEntry.Plugin -> append(indent).append("  <plugin id=\"").append(entry.id).append("\"/>\n")
         is DepEntry.Module -> append(indent).append("  <module name=\"").append(entry.name).append("\"/>\n")
+        is DepEntry.Comment -> append(indent).append("  ").append(entry.text).append("\n")
       }
     }
     if (autoPlugins.isNotEmpty() || autoModules.isNotEmpty()) {
diff --git a/platform/build-scripts/product-dsl/testSrc/xml/XmlDependencyUpdaterTest.kt b/platform/build-scripts/product-dsl/testSrc/xml/XmlDependencyUpdaterTest.kt
index 6c026d138a26..55aefa1a79fe 100644
--- a/platform/build-scripts/product-dsl/testSrc/xml/XmlDependencyUpdaterTest.kt
+++ b/platform/build-scripts/product-dsl/testSrc/xml/XmlDependencyUpdaterTest.kt
@@ -237,6 +237,73 @@ class XmlDependencyUpdaterTest {
     assertThat(xml).contains("<plugin id=\"new.plugin\"/>")
   }
 
+  @Test
+  fun `preserves placeholder comment when transitioning from no region to inside region`(@TempDir tempDir: Path) {
+    // Repro of IJI-2993-style regression: a plugin.xml with hand-authored placeholder comments
+    // and an explicit <dependencies> section but no generated region was rewritten by the
+    // generator, which dropped every comment along with the rebuilt block.
+    val content = """
+      <idea-plugin>
+        <id>org.example</id>
+        <name>Example</name>
+        <dependencies>
+          <!-- IJ/AS-DEPENDENCY-PLACEHOLDER -->
+          <plugin id="com.intellij.java"/>
+          <module name="intellij.platform.collaborationTools"/>
+        </dependencies>
+      </idea-plugin>
+    """.trimIndent()
+
+    val updater = DeferredFileUpdater(tempDir)
+    val path = tempDir.resolve("META-INF/plugin.xml")
+    updateXmlDependencies(
+      path = path,
+      content = content,
+      moduleDependencies = listOf("intellij.java.backend"),
+      pluginDependencies = emptyList(),
+      preserveExistingPlugin = { it == "com.intellij.java" },
+      preserveExistingModule = { it == "intellij.platform.collaborationTools" },
+      strategy = updater,
+    )
+
+    val xml = updater.getDiffs().single().expectedContent
+    assertThat(xml).contains("<!-- IJ/AS-DEPENDENCY-PLACEHOLDER -->")
+    assertThat(xml).contains("<plugin id=\"com.intellij.java\"/>")
+    assertThat(xml).contains("<module name=\"intellij.platform.collaborationTools\"/>")
+    assertThat(xml).contains("<module name=\"intellij.java.backend\"/>")
+    assertThat(xml.indexOf("<!-- IJ/AS-DEPENDENCY-PLACEHOLDER -->"))
+      .isLessThan(xml.indexOf("<!-- region Generated dependencies"))
+  }
+
+  @Test
+  fun `does not duplicate or re-emit fold region markers as comments`(@TempDir tempDir: Path) {
+    val content = """
+      <idea-plugin>
+        <id>org.example</id>
+        <name>Example</name>
+        <dependencies>
+          <!-- region Generated dependencies - run `Generate Product Layouts` to regenerate -->
+          <module name="intellij.platform.debugger.impl.ui"/>
+          <!-- endregion -->
+        </dependencies>
+      </idea-plugin>
+    """.trimIndent()
+
+    val updater = DeferredFileUpdater(tempDir)
+    val path = tempDir.resolve("META-INF/plugin.xml")
+    updateXmlDependencies(
+      path = path,
+      content = content,
+      moduleDependencies = listOf("intellij.platform.debugger.impl.ui", "intellij.platform.collaborationTools"),
+      pluginDependencies = emptyList(),
+      strategy = updater,
+    )
+
+    val xml = updater.getDiffs().single().expectedContent
+    assertThat(xml).containsOnlyOnce("<!-- region Generated dependencies")
+    assertThat(xml).containsOnlyOnce("<!-- endregion -->")
+  }
+
   @Test
   fun `removes duplicate legacy depends for modern plugin deps`() {
     val content = """