diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatCompilationResolverPlugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatCompilationResolverPlugin.kt
index c4fc3f51bc5..00c8e6f723f 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatCompilationResolverPlugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatCompilationResolverPlugin.kt
@@ -89,7 +89,9 @@ internal class DukatCompilationResolverPlugin(
 
         val target = compilation.target
         val externalsOutputFormat = compilation.externalsOutputFormat
-        if (target is KotlinJsTarget && externalsOutputFormat == ExternalsOutputFormat.SOURCE) {
+        val legacyTargetReuseIrTask =
+            target is KotlinJsTarget && (target.irTarget != null && externalsOutputFormat == ExternalsOutputFormat.SOURCE)
+        if (legacyTargetReuseIrTask) {
             return
         }
 
@@ -105,7 +107,7 @@ internal class DukatCompilationResolverPlugin(
     }
 
     companion object {
-        const val VERSION = "2"
+        const val VERSION = "3"
     }
 }
 
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatExecutor.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatExecutor.kt
index 32ac555e611..0984b51efd4 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatExecutor.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/dukat/DukatExecutor.kt
@@ -40,7 +40,7 @@ class DukatExecutor(
         versionFile.delete()
 
         npmProject.externalsDirRoot.mkdirs()
-        val inputs = typeDefinitions.joinToString("\n") { it.inputKey }
+        val inputs = "$externalsOutputFormat: " + typeDefinitions.joinToString("\n") { it.inputKey }
 
         if (!compareInputs || !inputsFile.isFile || inputsFile.readText() != inputs) {
             // delete file to run visit on error even without package.json updates