Having been working on this for a while now I have found that when our developers need to modify a DB to add a table or SP to the Merge Replication it fails unless it is deselected from the Transactional Replication beforehand. However when I de-select and re-select the article on the Transactional Publication it then breaks the Transactional Subscription and I have to re-create it every time.

Is there an easy way to get round the addition or change of articles? I'm even looking and using Merge Replication throughout but this is causing issues when I re-publish even though the above script has been run on the 1st publisher.