I'm running FTM 2014 on a Windows 7 (64-bit) laptop. I changed the name of the sync file so it no longer matched the filename of the FTM data file (e.g. MyFamily.sync -> Old-MyFamily.sync). You need to make sure you haven't started FTM first as the file will be in use.
Once you rename the sync file, when you open FTM, it will tell you that you haven't uploaded your file to Ancestry and will ask if you want to. Please note that any sharing, etc., will be lost so you will have to reestablish this. This was because there wasn't a sync file that matched the FTM file. I permitted FTM to upload the FTM file to Ancestry and made sure the tree on Ancestry was not the same tree (in my case I just added FTM 2014 to the name). FTM then uploaded and linked the two files. I made some small changes on the Ancestry side and things sync'd okay but I haven't made a lot of major changes as of yet.
The prior tree on Ancestry (assuming you changed the tree name) will still be there and you should unlink it (or even delete it as it is a duplicate). It still thinks it is linked in FTM. This will also depend if you've made a lot of changes in Ancestry that aren't in your FTM file. If you have, then I would recommend exporting the old tree from Ancestry. I have not tried to upload to the old tree in Ancestry. In my case, there were only a couple of experimental changes I made online that were not worth recovering.