diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3b53faaec..b415a7f42 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@
 - [#868](https://github.com/LayerManager/layman/issues/868) Fill table `map_layer` with relations between maps and [internal layers](doc/models.md#internal-map-layer) (layers published on this Layman instance). Relations to [external layers](doc/models.md#internal-map-layer) (layers of other servers) are not imported into the table.
 ### Changes
 - [#868](https://github.com/LayerManager/layman/issues/868) Endpoints [GET Publications](doc/rest.md#get-publications), [GET Layers](doc/rest.md#get-layers), [GET Workspace Layers](doc/rest.md#get-workspace-layers), [GET Maps](doc/rest.md#get-maps), [GET Workspace Maps](doc/rest.md#get-workspace-maps), [GET Workspace Layer](doc/rest.md#get-workspace-layer), [GET Workspace Map](doc/rest.md#get-workspace-map), [POST Workspace Layers](doc/rest.md#post-workspace-layers), [DELETE Workspace Layer](doc/rest.md#delete-workspace-layer), [DELETE Workspace Layers](doc/rest.md#delete-workspace-layers), [DELETE Workspace Map](doc/rest.md#delete-workspace-map), [DELETE Workspace Maps](doc/rest.md#delete-workspace-maps), [POST Workspace Maps](doc/rest.md#post-workspace-maps), [PATCH Workspace Layer](doc/rest.md#patch-workspace-layer), [PATCH Workspace Map](doc/rest.md#patch-workspace-map) and [WMS/WFS endpoints](doc/endpoints.md) respects [HTTP header `X-Forwarded-Prefix`](doc/client-proxy.md#x-forwarded-prefix-http-header) of the request in the response.
-- [#868](https://github.com/LayerManager/layman/issues/868) Relations between map and [internal layers](doc/models.md#internal-map-layer) are updated in `map_layer` table when calling [POST Workspace Maps](doc/rest.md#post-workspace-maps), [DELETE Workspace Map](doc/rest.md#delete-workspace-map), and [DELETE Workspace Maps](doc/rest.md#delete-workspace-maps).
+- [#868](https://github.com/LayerManager/layman/issues/868) Relations between map and [internal layers](doc/models.md#internal-map-layer) are updated in `map_layer` table when calling [POST Workspace Maps](doc/rest.md#post-workspace-maps), [PATCH Workspace Map](doc/rest.md#patch-workspace-map), [DELETE Workspace Map](doc/rest.md#delete-workspace-map), and [DELETE Workspace Maps](doc/rest.md#delete-workspace-maps).
 - [#880](https://github.com/LayerManager/layman/issues/880) Use Docker Compose v2 (`docker compose`) in Makefile without `compatibility` flag and remove `Makefile_docker-compose_v1` file. Docker containers are named according to Docker Compose v2 and may have different name after upgrade.
 - [#765](https://github.com/LayerManager/layman/issues/765) Stop saving OAuth2 claims in filesystem, use prime DB schema only.
 - [#893](https://github.com/LayerManager/layman/issues/893) It is possible to specify logging level by new environment variable [LAYMAN_LOGLEVEL](doc/env-settings.md#LAYMAN_LOGLEVEL). Default level is `INFO`.
diff --git a/src/layman/map/prime_db_schema/tasks.py b/src/layman/map/prime_db_schema/tasks.py
index bfefab593..6e05cdc66 100644
--- a/src/layman/map/prime_db_schema/tasks.py
+++ b/src/layman/map/prime_db_schema/tasks.py
@@ -3,7 +3,7 @@
 from layman import celery_app
 from layman.celery import AbortedException
 from layman.common import empty_method_returns_true
-from .util import insert_internal_layers
+from .util import ensure_internal_layers
 from .. import util, MAP_TYPE
 from ...common.prime_db_schema.publications import set_bbox
 
@@ -32,7 +32,7 @@ def refresh_file_data(
     set_bbox(workspace, MAP_TYPE, mapname, native_bbox, crs, )
 
     map_layers = util.get_layers_from_json(mapjson)
-    insert_internal_layers(workspace, mapname, map_layers)
+    ensure_internal_layers(workspace, mapname, map_layers)
 
     if self.is_aborted():
         raise AbortedException
diff --git a/src/layman/map/prime_db_schema/util.py b/src/layman/map/prime_db_schema/util.py
index bc4f7bbd3..e561391db 100644
--- a/src/layman/map/prime_db_schema/util.py
+++ b/src/layman/map/prime_db_schema/util.py
@@ -6,14 +6,31 @@
 DB_SCHEMA = settings.LAYMAN_PRIME_SCHEMA
 
 
-def insert_internal_layers(workspace, mapname, layers):
-    map_id = get_publication_info(workspace, MAP_TYPE, mapname, context={'keys': ['id'], })['id']
-    for layer_workspace, layer_name, layer_index in layers:
+def ensure_internal_layers(workspace, mapname, layers):
+    map_info = get_publication_info(workspace, MAP_TYPE, mapname, context={'keys': ['id', 'map_layers'], })
+    map_id = map_info['id']
+    db_layers = {(layer_dict['workspace'], layer_dict['name'], layer_dict['index'], ) for layer_dict in map_info['_map_layers']}
+
+    to_insert = set(layers) - db_layers
+    to_delete = db_layers - set(layers)
+
+    for layer_workspace, layer_name, layer_index in to_insert:
         insert_query = f'''
         insert into {DB_SCHEMA}.map_layer(id_map, layer_workspace, layer_name, layer_index) values (%s, %s, %s, %s);
         '''
         db_util.run_statement(insert_query, (map_id, layer_workspace, layer_name, layer_index,))
 
+    for layer_workspace, layer_name, layer_index in to_delete:
+        delete_query = f'''
+        delete from {DB_SCHEMA}.map_layer
+        where id_map = %s
+          and layer_workspace = %s
+          and layer_name = %s
+          and layer_index = %s
+          ;
+        '''
+        db_util.run_statement(delete_query, (map_id, layer_workspace, layer_name, layer_index,))
+
 
 def delete_internal_layer_relations(workspace, mapname):
     map_id = get_publication_info(workspace, MAP_TYPE, mapname, context={'keys': ['id'], })['id']
diff --git a/tests/asserts/final/publication/metadata.py b/tests/asserts/final/publication/metadata.py
index 622b1f0b1..1f0f6bd22 100644
--- a/tests/asserts/final/publication/metadata.py
+++ b/tests/asserts/final/publication/metadata.py
@@ -28,7 +28,7 @@
     'identifier',
     'map_endpoint',
     'map_file_endpoint',
-    'operates_on',
+    'operates_on',  # When sending map with no items after there were some items, items are not deleted (probably because of bug in Micka)
     'organisation_name',
     'publication_date',
     'reference_system',
diff --git a/tests/dynamic_data/publications/map_layer_relation/map_layer_relation_test.py b/tests/dynamic_data/publications/map_layer_relation/map_layer_relation_test.py
index 445bd4d6d..081b49d9a 100644
--- a/tests/dynamic_data/publications/map_layer_relation/map_layer_relation_test.py
+++ b/tests/dynamic_data/publications/map_layer_relation/map_layer_relation_test.py
@@ -81,6 +81,29 @@
             'operates_on': [LAYER_HRANICE_PRIVATE],
         },
     },
+    'patch_map_with_different_layers': {
+        'post_before_test_args': {
+            'file_paths': [os.path.join(DIRECTORY, 'internal_wms_and_wfs.json')],
+        },
+        'exp_before_rest_method': {
+            'map_layers': {
+                # layer, layer index, exists?
+                (LAYER_HRANICE, 1, True),
+                (LAYER_MISTA_NON_EXISTENT, 2, False),
+                (LAYER_HRANICE, 3, True),
+            },
+            'operates_on': [LAYER_HRANICE],
+        },
+        'rest_method': base_test_classes.RestMethodAll.PATCH,
+        'rest_args': {
+            'file_paths': [os.path.join(DIRECTORY, 'internal_hranice_private.json')],
+            'actor_name': PRIVATE_WORKSPACE,
+        },
+        'exp_after_rest_method': {
+            'map_layers': [(LAYER_HRANICE_PRIVATE, 1, True)],
+            'operates_on': [LAYER_HRANICE_PRIVATE],
+        },
+    },
 }