I wasn't thinking of other files, but e.g. a catkeys file known to be broken. Currently it can just be excluded in the Jamfile; when using globbing the file would need to be removed from the folder.
I never saw a file becoming broken on it's own, so it would still be possible to either revert to a previous version or resync from hta. The worst thing that can happen is a catalog being out of date, in this case you get an half-translated application. But it still works.
-- Adrien Destugues / PulkoMandy http://pulkomandy.ath.cx