I like to do the same thing, work in both. I started with online tree and then got ATM. Before syncing. I did get 2012 just for the syncing even though I had just bought 2011.
I downloaded my existing tree into FTM and uploaded a new one.. they are both on line actually. Hope no one looks at the old one since I do experiments with it.. I put up a warning.
But this is a long-winded way of saying that I never really have had a problem with syncing. I've learned a few things.. never cancel a sync, always stop the process. If online tree says syncing and FTM says it is ok, make a small change in FTM and then sync. I have restored from backup twice and syncing has resumed; have never had to un-link.
HOWEVER, I am now in the process of refining my FTM tree just in case. I have too many notes now in FTM to give it up, so I would not want to download my online tree, much rather make a new one from FTM. I am going through making sure all errors are fixed, and all media downloaded.
AND I am NOT using the new merge.
So I guess you could say that is my exit strategy even though I'm not actually planning to exit. But I don't trust online storage for all my hard work. What if the new owner decides to drop everything.. My data is saved on an external hard drive as well as my computer and another hard drive for back up. Should have an off site backup too. Besides AMT.