[Geoff Bacon]

From my time managing computer systems, one shouldn't be overwriting your only "backup" with your running system because, as you have found, you can end up with two damaged copies.

So, rather than synchronising, you should be using the MS backup option (I use it via the Companion). Historically, when using magnetic tapes, one would have at least 3 tapes and rotate them by overwriting the oldest each time. This meant that you still had somethnig to go back to if you didn't immediately notice that your system was corrupted.

For MS, I just take a new backup each time (my system is not "big" compared to others that I've read about) and periodically purge old versions (when I remember).

There is nothing to stop you synchronising every now and again as long as you aren't relying on this as the backup.
Obviously, this all depends on the size of your MS database/files.

Hopefully Mike will be able to sort out a way to restore what you had.

Geoff
PS:  I don't use synchronize