I don't know exactly how your synth will react. On a D-10 I changed the battery on the factory patches were fine after the change. Anything in user memory was wiped out, but you are already experiencing that. If your battery is dead, then I would have to guess that any damage has already been done.
If you change the battery and the factory patches are wiped out, you can do a factory reset by holding the TONE/FUNCTION and WRITE buttons down and powering on the synth (from a synth reset website http://www.dlse.nl/synthrepair/reset.html
) That will get the sounds/settings back to like when it was new.
Of course, diagnosis over the web is never perfectly accurate, and I can only guess from your information what the problem is. There is always at least a small risk factor in doing your own repairs.
Good luck, and let us know how it turns out.