I agree with Bob. I believe the larger a file is the more likely you will experience sync issues. I've done all you're recommended many times with success until recently. I have 48k people in my tree with 850k records and 30k media files. It's the size of the file. It takes me an hour and 32 minutes to sync my tree which I did faithfully every evening until 7 nights ago. Ancestry's fix? Split my tree. Probably not.
I've been digging into their sync log and reporting (as much as I can read). I found an error on a media file downloading from Ancestry. I removed it from Ancestry and from FTM2012. However, that same media file is showing up as a media error in in every sync log I've tried since. This has been reported to Ancestry Support.
The sync log file also has an anomoly in it. It's showing an error on a 1900 US Census union. It turns out to be the marriage fact associated with a husband and wife. I've removed that fact from both Ancestry and FTM2012. It also continues to show up in every sync even though that record does not exist. I would be curious to understand what these sync logs and reports are looking at.