I have chattahoochee stone on my pool deck. It is faded and all the smalls stone have come loose & hurts to walk on deck, plus dirt & mold forms where the stones have come off. Can I cover over it with some other material or do I have to remove the stone first?

Post a few pictures. In most cases it all needs to come out and be replaced.
Reason being nothings going to stay stuck to rounded stones.
It could be redone with stamped concrete to make it look like stone or brick, stained, or exposed agrigate.

too bad you didn't read the posts on c'stone before you installed it. If the stone is comming loose in places , it is sure to be deteriorating all over. I would use a high pressure washer to remove it. Use a washer that is capable of reaching 2500 pst. try to direct the pressure so it goes under the c'stone

Once the small stones start coming out it's the beginning of the end. You will need to replace it all.