diff --git a/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java b/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
index 83f8249f54..a11ec58c0c 100644
--- a/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
+++ b/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
@@ -598,14 +598,14 @@ abstract class AbstractGenerator implements Generator {
      * If file is a file, delete it.
      */
     protected void empty(File file, String suffix) {
-        empty(file, suffix, Collections.<File>emptySet());
+        empty(file, suffix, Collections.<File>emptySet(), Collections.<File>emptySet());
     }
 
     /**
      * If file is a directory, recursively empty its children.
      * If file is a file, delete it, except if it is in the list of files to keep.
      */
-    protected void empty(File file, String suffix, Set<File> keep) {
+    protected void empty(File file, String suffix, Set<File> keep, Set<File> ignore) {
         if (file != null) {
 
             // Just a Murphy's Law safeguard in case a user misconfigures their config...
@@ -614,12 +614,17 @@ abstract class AbstractGenerator implements Generator {
                 return;
             }
 
+            // [#5614] Don't go into these directories
+            for (File i : ignore)
+                if (file.getAbsolutePath().startsWith(i.getAbsolutePath()))
+                    return;
+
             if (file.isDirectory()) {
                 File[] children = file.listFiles();
 
                 if (children != null)
                     for (File child : children)
-                        empty(child, suffix, keep);
+                        empty(child, suffix, keep, ignore);
 
                 File[] childrenAfterDeletion = file.listFiles();
 
diff --git a/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java b/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
index 17ca720905..49f4ecdb09 100644
--- a/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
+++ b/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
@@ -176,10 +176,17 @@ public class JavaGenerator extends AbstractGenerator {
     private Map<CatalogDefinition, String> catalogVersions;
 
     /**
-     * All files modified by this generator
+     * All files modified by this generator.
      */
     private Set<File>                      files                        = new LinkedHashSet<File>();
 
+    /**
+     * These directories were not modified by this generator, but flagged as not
+     * for removal (e.g. because of {@link #schemaVersions} or
+     * {@link #catalogVersions}).
+     */
+    private Set<File>                      directoriesNotForRemoval     = new LinkedHashSet<File>();
+
     private final boolean                  scala;
     private final String                   tokenVoid;
 
@@ -271,7 +278,8 @@ public class JavaGenerator extends AbstractGenerator {
 
         // [#5556] Clean up common parent directory
         log.info("Removing excess files");
-        empty(getStrategy().getFileRoot(), (scala ? ".scala" : ".java"), files);
+        empty(getStrategy().getFileRoot(), (scala ? ".scala" : ".java"), files, directoriesNotForRemoval);
+        directoriesNotForRemoval.clear();
         files.clear();
     }
 
@@ -323,6 +331,10 @@ public class JavaGenerator extends AbstractGenerator {
             }
             else {
                 log.info("Existing version " + oldVersion + " is up to date with " + newVersion + " for catalog " + catalog.getInputName() + ". Ignoring catalog.");
+
+                // [#5614] If a catalog is not regenerated, we must flag it as "not for removal", because its contents
+                //         will not be listed in the files directory.
+                directoriesNotForRemoval.add(getStrategy().getFile(catalog).getParentFile());
                 return;
             }
         }
@@ -361,6 +373,10 @@ public class JavaGenerator extends AbstractGenerator {
             }
             else {
                 log.info("Existing version " + oldVersion + " is up to date with " + newVersion + " for schema " + schema.getInputName() + ". Ignoring schema.");
+
+                // [#5614] If a schema is not regenerated, we must flag it as "not for removal", because its contents
+                //         will not be listed in the files directory.
+                directoriesNotForRemoval.add(getStrategy().getFile(schema).getParentFile());
                 return;
             }
         }