The two timelines do not diverge until well after 1893 (even under my (crackpot?) theory that the divergence started in 2063 with the events of Star Trek: First Contact). So is Data's head - the head of a Data that served on the Prime timeline Enterprise-D - still under San Francisco, as shown in the TNG episode "Time's Arrow"? Pretty screwed up if it is, but I can't think of a good reason why it would not be.