diff --git a/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/IncrementalJpsTestGenerated.java b/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/IncrementalJpsTestGenerated.java
index e2d31966418..52e58a691ab 100644
--- a/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/IncrementalJpsTestGenerated.java
+++ b/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/IncrementalJpsTestGenerated.java
@@ -594,6 +594,11 @@ public class IncrementalJpsTestGenerated extends AbstractIncrementalJpsTest {
             runTest("jps-plugin/testData/incremental/multiModule/multiplatform/custom/commonSourcesCompilerArg/");
         }
 
+        @TestMetadata("complementaryFiles")
+        public void testComplementaryFiles() throws Exception {
+            runTest("jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/");
+        }
+
         @TestMetadata("notSameCompiler")
         public void testNotSameCompiler() throws Exception {
             runTest("jps-plugin/testData/incremental/multiModule/multiplatform/custom/notSameCompiler/");
@@ -638,6 +643,19 @@ public class IncrementalJpsTestGenerated extends AbstractIncrementalJpsTest {
             }
         }
 
+        @TestMetadata("jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles")
+        @TestDataPath("$PROJECT_ROOT")
+        @RunWith(JUnit3RunnerWithInners.class)
+        public static class ComplementaryFiles extends AbstractIncrementalJpsTest {
+            private void runTest(String testDataFilePath) throws Exception {
+                KotlinTestUtils.runTest(this::doTest, TargetBackend.ANY, testDataFilePath);
+            }
+
+            public void testAllFilesPresentInComplementaryFiles() throws Exception {
+                KotlinTestUtils.assertAllTestsPresentByMetadata(this.getClass(), new File("jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles"), Pattern.compile("^([^\\.]+)$"), TargetBackend.ANY, true);
+            }
+        }
+
         @TestMetadata("jps-plugin/testData/incremental/multiModule/multiplatform/custom/notSameCompiler")
         @TestDataPath("$PROJECT_ROOT")
         @RunWith(JUnit3RunnerWithInners.class)
diff --git a/jps-plugin/src/org/jetbrains/kotlin/jps/build/FSOperationsHelper.kt b/jps-plugin/src/org/jetbrains/kotlin/jps/build/FSOperationsHelper.kt
index 6be8361cce3..51ff82208df 100644
--- a/jps-plugin/src/org/jetbrains/kotlin/jps/build/FSOperationsHelper.kt
+++ b/jps-plugin/src/org/jetbrains/kotlin/jps/build/FSOperationsHelper.kt
@@ -19,7 +19,9 @@ package org.jetbrains.kotlin.jps.build
 import com.intellij.openapi.diagnostic.Logger
 import com.intellij.util.containers.ContainerUtil
 import org.jetbrains.jps.ModuleChunk
+import org.jetbrains.jps.builders.BuildRootDescriptor
 import org.jetbrains.jps.builders.BuildTarget
+import org.jetbrains.jps.builders.java.JavaSourceRootDescriptor
 import org.jetbrains.jps.builders.java.dependencyView.Mappings
 import org.jetbrains.jps.incremental.CompileContext
 import org.jetbrains.jps.incremental.FSOperations
@@ -27,6 +29,7 @@ import org.jetbrains.jps.incremental.ModuleBuildTarget
 import org.jetbrains.jps.incremental.fs.CompilationRound
 import java.io.File
 import java.util.HashMap
+import kotlin.collections.*
 
 /**
  * Entry point for safely marking files as dirty.
@@ -76,10 +79,13 @@ class FSOperationsHelper(
     fun markFilesForCurrentRound(target: ModuleBuildTarget, files: Iterable<File>) {
         require(target in chunk.targets)
 
-        val targetDirtyFiles = dirtyFilesHolder.byTarget[target]!!
-        files.forEach {
-            val root = compileContext.projectDescriptor.buildRootIndex.findJavaRootDescriptor(compileContext, it)!!
-            targetDirtyFiles._markDirty(it, root)
+        val targetDirtyFiles = dirtyFilesHolder.byTarget.getValue(target)
+        files.forEach { file ->
+            val root = compileContext.projectDescriptor.buildRootIndex
+                .findAllParentDescriptors<BuildRootDescriptor>(file, compileContext)
+                .single { sourceRoot -> sourceRoot.target == target }
+
+            targetDirtyFiles._markDirty(file, root as JavaSourceRootDescriptor)
         }
 
         markFilesImpl(files, currentRound = true) { it.exists() }
diff --git a/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/_dependencies.txt b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/_dependencies.txt
new file mode 100644
index 00000000000..4d7c19bc98d
--- /dev/null
+++ b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/_dependencies.txt
@@ -0,0 +1,4 @@
+c [sourceSetHolder]
+
+pJvm [compilationAndSourceSetHolder, jvm]
+pJvm -> c [include]
\ No newline at end of file
diff --git a/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/build.log b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/build.log
new file mode 100644
index 00000000000..55fe16560c0
--- /dev/null
+++ b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/build.log
@@ -0,0 +1,14 @@
+================ Step #1 =================
+
+Building c
+Building pJvm
+Cleaning output files:
+  out/production/pJvm/FJvmKt.class
+  out/production/pJvm/META-INF/pJvm.kotlin_module
+End of files
+Compiling files:
+  c/src/f.kt
+  pJvm/src/fJvm.kt
+End of files
+Exit code: OK
+------------------------------------------
\ No newline at end of file
diff --git a/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/c_f.kt b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/c_f.kt
new file mode 100644
index 00000000000..8cd923f49e2
--- /dev/null
+++ b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/c_f.kt
@@ -0,0 +1,9 @@
+expect fun f()
+
+@ExperimentalMultiplatform
+@OptionalExpectation
+internal expect annotation class SharedImmutable()
+
+@ExperimentalMultiplatform
+@SharedImmutable
+val UNDEFINED = 1
\ No newline at end of file
diff --git a/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt
new file mode 100644
index 00000000000..28071449f08
--- /dev/null
+++ b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt
@@ -0,0 +1,3 @@
+actual fun f() = Unit
+
+fun x() = 1
\ No newline at end of file
diff --git a/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt.new.1 b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt.new.1
new file mode 100644
index 00000000000..882aadc875c
--- /dev/null
+++ b/jps-plugin/testData/incremental/multiModule/multiplatform/custom/complementaryFiles/pJvm_fJvm.kt.new.1
@@ -0,0 +1,3 @@
+actual fun f() = Unit
+
+fun x() = 2
\ No newline at end of file