I don't believe your Gedcom difficulties have anything to do with syncing.
There are a lot of folks here who seem to have sync working for them with no problems. But, there are still enough with nightmarish difficulties that I'm not going to sync my file. Why should I take the chance? I would get nothing from uploading to ancestry that I can't get from WorldConnect.
How many people are in your file?
1) Can you create a backup (include images) without a problem?
2) Can you do an FTM export (include images) without a problem? (I would export to a separate directory.)
3) Can you create a new file, add one person and get a gedcom out of that one person file?
If you can do the last one, that suggests there is some element of corruption in your current file.
If you are able to successfully do the export to FTM with images above, I would bring it up and see if that will export a gedcom. If it does, I would start using that as my new main file. Be sure you give the old file a new name (maybe the old file name with today's date to indicate it is frozen.)
If you were not able to get the exported file to work, but were able to do a backup with images, I would attempt to restore it, in a different folder and see if that will create a gedcom. If it does, I would start using that file and rename the old file with today's date in the name.)
Post back your results here, if you don't mind, so that we can see if any of these worked.