Or you could use a bushing. That would be the best method. Filling and drilling can result in enough off-center error to cause serious problems. What are your motor shaft OD and encoder ID?
Brewgyver:
Filling and drilling can result in enough off-center error to cause serious problems.
Well - you just gotta be a bit smart about it:
Find the diameter of the hole, then find a drill or piece of steel rod that matches hole (hopefully it is a standard diameter)
Mount said drill in drill press (verify that drill press table is square with chuck)
Put a piece of wax paper over a piece of wood and clamp or otherwise afix it to the drill press table
Bring the rod down to pass thru the center of the encoder disk until it touches the wood/wax paper; lock the chuck position in place
Clamp or otherwise afix the encoder disk to the the wood so it can't move
Unlock and raise the chuck/rod - remove the rod from the chuck (be careful to not disturb the position of the wood/encoder/table, etc)
Fill in the center of the encoder disk with the epoxy (again, be careful not to disturb/move anything - if you've clamped things properly, this shouldn't be an issue)
Once the epoxy is fully cured, put a drill the size (or slightly smaller for a press fit) of the motor shaft into the drill press chuck
Drill out the center of the epoxy
Provided nothing was disturbed after step 5, the new hole should be fairly concentric with the original hole; it won't likely be perfect, but it won't wobble all over the place, either.
Then again, if a bushing can be found that works (and is inexpensive enough), then it would probably be easier to use...
I've made paper bushings for small motor shafts when a lot of shaft torque isn't required. Cut a strip of paper that is a little wider than the motor shaft. Tightly wrap the paper strip around the shaft, then try to press on the encoder wheel. If it is too tight, snip off a little off the end of the paper strip, rewrap, and try the fit again. Keep snipping until you get a snug fit on the shaft. Pull the the paper with the wheel on it out just a little so the paper bushing doesn't rub on the motor housing. A little trimming and maybe a drop of crazy glue should hold the wheel in place.