I'm lost. I thought you were talking about merging an ancestry census record into FTM. But now you have started talking about synchronization - which is a whole other issue.
It is the standard procedure for an ancestry census record (even in the UK) to post the SEX census fact for a person, as well as the census citation for that fact. I just did it for the Mary Hallock example that I posted earlier.
Now I am wondering if you are saying that you are merging the record to a person in an ancestry member tree and the fact and the citation are not being synced???
I can't help you there. I don't sync my files because of all the problems they have. You can easily copy and paste either facts or citations from one person to another in FTM. Or, you can choose to ignore the sex except where you have a bi-sexual name like Leslie or Frances. Back in the day when we posted micro-film censuses manually into FTM, most of us didn't post sex into FTM, unless there was a need to clarify the sex of the person - because it is obvious 95% of the time.