It sounds like the typical feature (bug) that you should expect after awhile. If it's Near 100% repeatable, you're lucky. Now you know what to look for. Periodically, and I mean somewhere between 1 and 99 times out of a hundred, I (and several folks I know) lose binding information, maps, and pipelines after deploying. Since this occurs in dev so often, I make sure to save Bindings regularly and even search-and-replace ****** with the actual (single) password every time I save it…but I still check on import or before adding to resources in the application.
Have you informed Microsoft about this? You may as well add it to the pile just so someone gets a chance to look at it.