I too worked for pep boys a long time ago, it was nice to up-sell people $100 for the flush. I've heard that the pressure from the flush can break things loose and kill the transmission, I am on the fence, I've never had it done.

I am an advocate of doing a drop the pan, change the filter, refill fluid, and going. If the fluid was really nasty, do the same service again in a few weeks, so you exchange more fluid.

To the OP... I'd change the fluid and filter.