It may require some truss rod adjustment, maybe some intonation tweaking as well, but nothing you shouldn't be able to handle yourself if you read up on how to do it. And it may be fine.

There's going to be a difference in total string tension. 9-46s are close to 100 lb. total in standard tuning on a Fender-scale, a couple pounds less on a Gibson-scale. 9-42s are about 90 lb. on a Fender-scale. (I calculated several different string set tensions & wrote them down long ago.)

I don't know about 11-54s in Drop-C -- is that like Drop-D but 2 semitones lower? I know that 11-54s are about 113 pounds tuned 2 semitones down from standard on a Gibson scale, haven't calculated it on a Fender scale but it should be about 5-7 pounds heavier. Drop the 6th string 2 semitones from that and it'll go down about 4 pounds, so my estimate of 11-54s in Drop-C on a Fender-scale is around 115 pounds.

A change of about 15% in total string tension might require a small tightening of the truss rod. Check your neck relief at the 8th fretbefore doing the change; if it goes up significantly after that (wait a day for the tension to settle) you might want to tighten it a little; start with 1/8" of a turn & go from there. Though a little more relief might be necessary to prevent buzzing, so you might want to just leave it if the action in the middle of the neck isn't too high. Check intonation after doing all that and adjust if necessary.