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cybmole - why don't you ask the folks at FFS, I've found them to be responsive and very helpful.
But as far as I can tell, a file is only removed from the mirror if its removed from the source, not if a filter is applied. Filters can be turned off and reinstated, so filters not removing what's on the mirror makes sense to me. Also the three incremental file synch products with which I'm familiar (FFS, Good Synch and Cheetah) all work the same.
IMO its best to keep backups as 'vanilla' as possible. It's almost inevitable that you'll be 'stressed' when you need them, so the fewer the exceptions the better. I'd rather find something in the backup that I don't need, rather than fail to find something I do need
Regarding Google. Products don't get customer service, customers get that, another pair of eyeballs is just another product they can sell to their customers - advertising agencies and multi-nat marketeers. TINSTAAFL thrives in Mountain View CA
BR