The update surely won't remove any AFCAD from FSDT, it might just update them to the latest version.
Have you possibly set some folders with a DONTUPDATE file ? This would prevent the update to do its job and, basically, shouldn't be don, but we added this (not documenting it and with a strong suggestion NOT to use it) because users want to modify our AFCAD.
Remove all your DONTUPDATE files, if you have any, and do the update again.
