I'm a bit confused. When you found that your FTM file had all these problems, why didn't you trash it and use:
2) Your ancestry file - just download it as a separate file to your hard drive.
You said: "My question: since I'm pretty sure you can't tell FTM to sync only one way
Sure, the good, old-fashoned one-way uploading and downloading is still available. You upload at in the Websearch workspace, upper right corner: share. From ancestry.com download to your hard drive as an FTM file (don't need a gedcom), you access at your on-line tree under Settings.
So, I take it you now have two good files? One is ancestry and one is in ftm? And they both are supposed to be in synch but you have sync on manual? I would break the sync. I think you can do that by creating a new directory and then copying your ftm file and related media folder to it. Then leave the current ancestry tree and "old" ftm file as "archival" backups for awhile. Then upload your "new" FTM (via share, not sync) to ancestry.
I've heard too many scary stories, like yours, about sync. I am not using it. I still like WorldConnect. It shows alternative names in the index and it allows the host to be able to say whether viewers can download anything or not. (I choose not.) You don't have that choice with an ancestry tree. People can "take" your stuff only one family at a time, but over an afternoon, they can take quite a few families of your work.