diff --git a/layerindex/update.py b/layerindex/update.py
index dd794dd..72bad6c 100755
--- a/layerindex/update.py
+++ b/layerindex/update.py
@@ -128,7 +128,7 @@ def print_subdir_error(newbranch, layername, vcs_subdir, branchdesc):
     if newbranch:
         logger.info("Skipping update of layer %s for branch %s - subdirectory %s does not exist on this branch" % (layername, branchdesc, vcs_subdir))
     elif vcs_subdir:
-        return "Subdirectory for layer %s does not exist on branch %s - if this is legitimate, the layer branch record should be deleted" % (layername, branchdesc)
+        return "Subdirectory %s for layer %s does not exist on branch %s" % (vcs_subdir, layername, branchdesc)
     return None
 
 def extract_value(valuename, output):
@@ -291,6 +291,15 @@ def main():
         if not options.dryrun:
             layerupdate.save()
 
+    def disable_layerbranch_updates(layer, branchobj, layerbranch, msg):
+        """The layer has gone from this branch: record why and stop updating
+        it. Unlike deleting the layer branch, this keeps its data and can be
+        undone by enabling updates again."""
+        if not options.dryrun:
+            layerbranch.updates_enabled = False
+            layerbranch.save(update_fields=['updates_enabled'])
+        record_layer_error(layer, branchobj, '%s - updates for this layer branch have been disabled' % msg)
+
     try:
         lockfn = os.path.join(fetchdir, "layerindex.lock")
         lockfile = utils.lock_file(lockfn, options.timeout, logger)
@@ -442,7 +451,7 @@ def main():
                         if not topcommit:
                             errmsg = print_subdir_error(newbranch, layer.name, layerbranch.vcs_subdir, branchdesc)
                             if errmsg:
-                                record_layer_error(layer, branchobj, errmsg)
+                                disable_layerbranch_updates(layer, branchobj, layerbranch, errmsg)
                             if not (newbranch and layerbranch.vcs_subdir):
                                 record_layer_error(layer, branchobj, "Failed to get last revision for layer %s on branch %s" % (layer.name, branchdesc))
                             continue
@@ -462,11 +471,15 @@ def main():
                         if layerbranch.vcs_subdir and not os.path.exists(layerdir):
                             errmsg = print_subdir_error(newbranch, layer.name, layerbranch.vcs_subdir, branchdesc)
                             if errmsg:
-                                record_layer_error(layer, branchobj, errmsg)
+                                disable_layerbranch_updates(layer, branchobj, layerbranch, errmsg)
                             continue
 
                         if not os.path.exists(os.path.join(layerdir, 'conf/layer.conf')):
-                            record_layer_error(layer, branchobj, "conf/layer.conf not found for layer %s (branch %s) - is subdirectory set correctly?" % (layer.name, branch))
+                            errmsg = "conf/layer.conf not found for layer %s (branch %s) - is subdirectory set correctly?" % (layer.name, branch)
+                            if newbranch:
+                                record_layer_error(layer, branchobj, errmsg)
+                            else:
+                                disable_layerbranch_updates(layer, branchobj, layerbranch, errmsg)
                             continue
 
                     fd, initial_fn = tempfile.mkstemp(prefix='layerindex-initial-')
diff --git a/tests/test_update.py b/tests/test_update.py
index 3266d44..8cd3161 100644
--- a/tests/test_update.py
+++ b/tests/test_update.py
@@ -173,18 +173,19 @@ def test_initial_values_not_in_output(import_layer):
     assert 'BBFILE_COLLECTIONS = ' not in result.stdout
     assert 'Unable to find BBFILE_COLLECTIONS' not in result.stdout
 
-def set_layerbranch(subdir, last_rev):
+def set_layerbranch(subdir, last_rev, updates_enabled=True):
     # In a separate process, so that update.py sees the change: the tests run
     # in a transaction
     run_cmd('python3 manage.py shell -c "from layerindex.models import LayerBranch; '
             'LayerBranch.objects.filter(layer__name=\'meta-layerindex-test\').update('
-            'vcs_subdir=\'%s\', vcs_last_rev=\'%s\')"' % (subdir, last_rev), cwd=basepath)
+            'vcs_subdir=\'%s\', vcs_last_rev=\'%s\', updates_enabled=%s)"' % (subdir, last_rev, updates_enabled), cwd=basepath)
 
 def test_first_parse_error_recorded_against_layer(import_layer, repo, db_access_without_rollback_and_truncate):
     # [YOCTO #13490] an error that stops a layer being parsed is recorded
     # in the layer's update history, not only in the overall update log
     from layerindex.models import LayerBranch, LayerUpdate
     layerbranch = LayerBranch.objects.get(layer__name='meta-layerindex-test')
+    saved = (layerbranch.vcs_subdir, layerbranch.vcs_last_rev)
     set_layerbranch('meta-layerindex-test/recipes-example', '')
     try:
         result = subprocess.run("layerindex/update.py -l meta-layerindex-test --nofetch --nocheckout",
@@ -193,8 +194,12 @@ def test_first_parse_error_recorded_against_layer(import_layer, repo, db_access_
         layerupdate = LayerUpdate.objects.filter(layer=layerbranch.layer).order_by('-id').first()
         assert 'conf/layer.conf not found for layer meta-layerindex-test' in layerupdate.log, result.stdout
         assert layerupdate.errors == 1
+        # [YOCTO #12922] the layer has gone from the branch: stop updating it
+        assert 'updates for this layer branch have been disabled' in layerupdate.log
+        layerbranch.refresh_from_db()
+        assert not layerbranch.updates_enabled
     finally:
-        set_layerbranch(layerbranch.vcs_subdir, layerbranch.vcs_last_rev)
+        set_layerbranch(*saved)