If the guitar was set up for 10-46 previously and you change to 9-46, there will be a little less total string tension. That means the trem will be angled back a little into the body. You will need to loosen the trem claw screws (that will be a trial and error process; loosen-tune-check-repeat, until the bridge is approximately parallel with the top of the guitar when you are tune.) You may need to loosen the truss rod a little if you get string buzz on the lower frets. Intonation will need to be adjusted on the lighter gauge strings but not drastically so: if you're ears think you're fine, you're good to go.
(obviously, if you go from 9-42 to 9-46, the wound strings will have more tension and you'll have to do the opposite adjustments to what I've said above).
All clear?