Cannot edit Document Template (.dotx) after template has been merged in a job and is now .docx

Check if the Cache Merge Templates Locally option is set in Manage Application Settings. 

With this option enabled, when a user merges a document, it actually makes a copy of the template and stores it in the users Temp folder. So when preparing docs the only template that should be locked will be the users temp copy and not the copy in your Merge Templates folder.