Not sure quite what you mean there!
Did you find runout on the chuck's internal taper, and damage to it, or was the damaged surface the *spindle* taper you put the chuck into? I'm guessing it's an ER40-on-a-stick with a Morse taper and drawbar into the spindle?
If it's the *spindle* internal Morse taper that's damaged, you could run a Morse taper reamer in from the tailstock end to clean it up, if necessary - if there's just a small burr or three (which is enough to put the chuck off centre) you may be able to clean it up with a three-square scraper[1]. To check whether it's just a burr, put marking blue (if you have it, if not a marker pen will do a passable job) on the chuck's Morse taper, fit it and give it a slight twist in the spindle. Any burrs will leave a clear spot that'll point you to where they are
If it's the chuck taper the best would be to internal grind it - although this would mean facing the open end of the chuck to get the correct taper gauge length.
[1] take a worn-out riffler file (the pointy curved ones, triangular in cross-section) and heat to "boiled carrots", leave to cool as slowly as possible, then grind / file off the teeth, hone to get sharp edges, harden by heating to "boiled carrots" again and quenching in oil - then hone the edges again to get 'em *really* sharp. This'll leave it really brittle, so careful!, but it should be hard enough to scrape the burrs down.
Dave H. (the other one)
Dave H. (the other one)