diff --git a/src/services/backend_script_api.js b/src/services/backend_script_api.js
index 620f6480f..c430c9f88 100644
--- a/src/services/backend_script_api.js
+++ b/src/services/backend_script_api.js
@@ -282,9 +282,10 @@ function BackendScriptApi(currentNote, apiParams) {
      * This method looks similar to toggleNoteInParent() but differs because we're looking up branch by prefix.
      *
      * @method
+     * @deprecated - this method is pretty confusing and serves specialized purpose only
      * @param {string} noteId
      * @param {string} prefix
-     * @param {string} [parentNoteId]
+     * @param {string|null} parentNoteId
      */
     this.setNoteToParent = treeService.setNoteToParent;
 
diff --git a/src/services/consistency_checks.js b/src/services/consistency_checks.js
index 9393b6224..5d0a286dd 100644
--- a/src/services/consistency_checks.js
+++ b/src/services/consistency_checks.js
@@ -195,7 +195,7 @@ async function findExistencyIssues() {
       HAVING
         COUNT(*) > 1`,
     async ({noteId, parentNoteId}) => {
-        const branches = await repository.getEntities(`SELECT * FROM branches WHERE noteId = ? and parentNoteId = ? and isDeleted = 1`, [noteId, parentNoteId]);
+        const branches = await repository.getEntities(`SELECT * FROM branches WHERE noteId = ? and parentNoteId = ? and isDeleted = 0`, [noteId, parentNoteId]);
 
         // it's not necessarily "original" branch, it's just the only one which will survive
         const origBranch = branches[0];
diff --git a/src/services/tree.js b/src/services/tree.js
index ca2459ac7..5a38c97a9 100644
--- a/src/services/tree.js
+++ b/src/services/tree.js
@@ -36,7 +36,7 @@ async function validateParentChild(parentNoteId, childNoteId, branchId = null) {
 }
 
 async function getExistingBranch(parentNoteId, childNoteId) {
-    return await sql.getRow('SELECT * FROM branches WHERE noteId = ? AND parentNoteId = ? AND isDeleted = 0', [childNoteId, parentNoteId]);
+    return await repository.getEntity('SELECT * FROM branches WHERE noteId = ? AND parentNoteId = ? AND isDeleted = 0', [childNoteId, parentNoteId]);
 }
 
 /**
@@ -123,6 +123,9 @@ async function sortNotesAlphabetically(parentNoteId, directoriesFirst = false) {
     });
 }
 
+/**
+ * @deprecated - this will be removed in the future
+ */
 async function setNoteToParent(noteId, prefix, parentNoteId) {
     const parentNote = await repository.getNote(parentNoteId);
 
@@ -151,11 +154,19 @@ async function setNoteToParent(noteId, prefix, parentNoteId) {
             throw new Error(`Cannot create a branch for ${noteId} which is deleted.`);
         }
 
-        await new Branch({
-            noteId: noteId,
-            parentNoteId: parentNoteId,
-            prefix: prefix
-        }).save();
+        const branch = await repository.getEntity('SELECT * FROM branches WHERE isDeleted = 0 AND noteId = ? AND parentNoteId = ?', [noteId, parentNoteId]);
+
+        if (branch) {
+            branch.prefix = prefix;
+            await branch.save();
+        }
+        else {
+            await new Branch({
+                noteId: noteId,
+                parentNoteId: parentNoteId,
+                prefix: prefix
+            }).save();
+        }
     }
 }