Before you worry about retiming the screws, you need to fix whatever has put them out of time. It is most unlikely that the bottom of the screw head or the screw's seat wore out. It is much more likely that something "moved." If, however, the "move" is permanent, then you will need to weld up the bottom of the screw head and recut or do the same for the seat. Or, you can make a new screw. You can't change timing of the screw by filing (shortening) the screw's threaded shank. The index between the threads and the screw slot doesn't depend on the length of the screw shank; no relationship at all. Indexing the slot to the threads would be a very tough machining problem if it were not for the use of "tall" screw heads that are cut off and reslotted after the screws final tightened position is clear.
