Your experience is why I advised the original poster to not change sources coming from FTM merges from ancestry.com databases.
There can be unintended consequences of changing what FTM posted - so I recommend leaving them alone. After all, what is wrong with mulitple instances of the same source? They don't hurt anything. It's strictly an "under the hood" issue which is not visible in reports.
PS - later change. I do change CITATIONS coming from ancestry databases, however - and have not noticed any detrimental consequences yet - although I don't sync. The biggest reason is for censuses that don't show the page number in the citation - very frustrating. There are many of them.