"That action caused FTM to create a new sync file whereas deleting the old Ancestry tree and uploading a new copy would not necessarily create a new sync file. "
I thought about this a little more. As you wrote yourself, when you "upload, link and sync an FTM file to an Ancestry tree, it creates a sync file on your local system." Does FTM, perhaps, use the same file name and then not overwrite the previous file with the same name? I think your proposition about it should be tested; otherwise, your solution isn't doing anything for those people with persistently fault links from FTM to Ancestry.com.
It sounds reasonable to me that these sync files, as part of the process of synchronizing, are one of the potential points of failure. My guess, however, is that the majority of failures results from unhandled exceptions in the code. ;)