diff --git a/docs/runtime/ir-caching.md b/docs/runtime/ir-caching.md
index 152cdbe6ba8..b4a8a6c07e5 100644
--- a/docs/runtime/ir-caching.md
+++ b/docs/runtime/ir-caching.md
@@ -171,6 +171,10 @@ Every `Persistance` class has a unique identifier. In order to keep definitions
 consistent one should not attempt to use smaller `id`s than previously assigned.
 One should also not delete any `Persistance` classes.
 
+Additionally, `PerMap.serialVersionUID` version provides a seed to the version
+stamp calculated from all `Persistance` classes. Increasing the
+`serialVersionUID` will invalidate all caches.
+
 ## Loading the IR
 
 Loading the IR is a multi-stage process that involves performing integrity
diff --git a/engine/runtime-compiler/src/main/scala/org/enso/compiler/data/BindingsMap.scala b/engine/runtime-compiler/src/main/scala/org/enso/compiler/data/BindingsMap.scala
index 1ac00671850..ed8010912e6 100644
--- a/engine/runtime-compiler/src/main/scala/org/enso/compiler/data/BindingsMap.scala
+++ b/engine/runtime-compiler/src/main/scala/org/enso/compiler/data/BindingsMap.scala
@@ -21,10 +21,6 @@ import scala.annotation.unused
   * @param definedEntities the list of entities defined in the current module
   * @param currentModule the module holding these bindings
   */
-
-@SerialVersionUID(
-  9057L // Use BindingsMap
-)
 case class BindingsMap(
   definedEntities: List[DefinedEntity],
   currentModule: ModuleReference
diff --git a/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java b/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
index f209b534de0..1f446a948fc 100644
--- a/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
+++ b/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
@@ -1,6 +1,5 @@
 package org.enso.compiler.core;
 
-import java.io.Serializable;
 import java.util.UUID;
 import java.util.function.Function;
 import org.enso.compiler.core.ir.DiagnosticStorage;
@@ -28,9 +27,7 @@ import scala.collection.immutable.List;
  *
  * <p>See also: Note [IR Equality and hashing]
  */
-public interface IR extends Serializable {
-
-  long serialVersionUID = 9057L; // Scala to Java
+public interface IR {
 
   /**
    * Storage for metadata that the node has been tagged with as the result of various compiler
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
index 3bf03f2465f..6c02caccbce 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
@@ -19,9 +19,6 @@ import java.util.UUID
   * @param passData    the pass metadata associated with this node
   * @param diagnostics compiler diagnostics for this node
   */
-@SerialVersionUID(
-  9057L // Use BindingsMap
-)       // prevents reading broken caches, see PR-3692 for details
 final case class Module(
   imports: List[Import],
   exports: List[Export],
diff --git a/lib/java/persistance/src/main/java/org/enso/persist/PerMap.java b/lib/java/persistance/src/main/java/org/enso/persist/PerMap.java
index fd640994c1f..253884d825e 100644
--- a/lib/java/persistance/src/main/java/org/enso/persist/PerMap.java
+++ b/lib/java/persistance/src/main/java/org/enso/persist/PerMap.java
@@ -7,6 +7,8 @@ import java.util.Map;
 import org.openide.util.lookup.Lookups;
 
 final class PerMap {
+
+  private static final int serialVersionUID = 8689; // Use PR number
   private static final Collection<? extends Persistance> ALL;
 
   static {
@@ -20,7 +22,7 @@ final class PerMap {
   final int versionStamp;
 
   private PerMap() {
-    int hash = 0;
+    int hash = serialVersionUID;
     for (var orig : ALL) {
       var p = orig.newClone();
       var prevId = ids.put(p.id, p);