My ganglion cyst is gone but now my wrist hurts and is weak since the last cyst went away, could there be damage?

Painful ganglion. The cyst wall may still be present and just deflated. A ganglion is the result of other underlying pathology such as arthritis, tendinitis, or a sprained ligament with a capsular tear. A thorough exam and some imaging studies can narrow down the potential causes, and if addressed can minimize recurrences.
Arthritis or tendon. A ganglion cyst forms generally as a result of degenerative changes involving a tendon structure or from a joint that is degenerating. It could also be a combination of both. If it remains symptomatic you should see an orthopedic surgeon, rheumatologist or physiatrist for a diagnosis and treatment.
Depends. Depends on how the cyst was taken care of, ie surgery, hit with a book, etc. There may be scar tissue or residual inflammation which should resolve over time.