If theres nothing wrong with the machine theres no need to do it... why risk failure for no improvement?
I havent heard of it being bad to flash them too much, but the more you do it the more chance you do have of a failed flash which in some cases will leave you with a paper weight.
Taking out the battery and the jumper setting would have cleared the CMOS. THIS HAS NOTHING TO DO WITH BIOS FLASHING. These are purely the setting that are in the Bios, hence why it resolved your RAM issue as settings would have gone back to default.