I always flush transmissions. I drop the pan and filter first, If their is not any junk in the pan, Its safe.
So many have the mentality that a full fluid change out on the a transmission is going to kill it. That reasoning is in place because how many people with cars have gotten their transmission fluid changed right when they noticed the transmissions performance degrading? Usually that issue is a tell tale sign that the transmission is on the way out. The NEW fluid had nothing to do with it.. The transmission was neglected or overheated too many times before hand.
I keep fresh ATF in every 4L60E here and change the fluid every 30-50,000 miles. I have 4, 4l60's
If the transmission is a piece of crap, Its a piece of crap.. If its a good transmission, NEW fluid is not going to hurt it. If its a piece of crap with burnt smelling transmission fluid, Forget it. Its on its way out because its been overheated.
Anyway.. Yes, Change the Filter, clean pan and refill the transmission. Run it around, then you can if you want run about 12 -14 quarts of new ATF through it. I have a measuring jar and I remove one of the lines off the transmission cooler. I pump out TWO quarts... Shut the car, ADD two quarts, Repeat until finished. Some PUMP out 4 quarts at a time. I dont like to do this because the pump is just about sucking nothing but air. 2 quarts at a time is Alot safer... You will never get the transmission fluid 100% clean as new mixes with the old.. Overall, The fluid will be in better condition after this is done.