Actually, the flight mechanism of flying squirrels is completely different than that of bats-- bats wings are long fingers, essentially, while flying squirrels and sugar gliders use loose underarm skin. Morphologically, they structures are as different as a squid's tentacles and an elephant's trunk, despite similar uses.

And you bring up my original objection: "At some point along the line, one subgroup or another becomes genetically incompatible with the rest." If evolution occurs due to mutation, and mutation occurs to single individuals, with whom do these mutated individuals breed? Whether it happens fast or slow, somewhere along the line there must be one individual that is incapable of reproducing with its breeding group, so how are those genes transmitted? A random mutation cannot happen to a large group of individuals at once.