I have never seen this before. The connections.xml used is the one saved in the app dir.
What is the error you get in automation when this happens? Send me log files.
What does the connection manager look like when you open TDP? Are you actually seeing them not displayed in the connection list? If the connections.xml got corrupted, I do no think any of the connections would work.
It is possible that the code in the automation script that tries to resolve a connection is not working because of some other connection that is similiar.
To debug this I would go to my App Dir (from the About Box) and rename my connections.xml. This will save your production copy. Then import in only the connections you need for the automation script. See if this stops the issue from occuring.
If so, then you would need to determine what similar connection is in the list that is causing the problem (same server but different database, different alias, etc)