When you intonate a guitar you are tuning it - from the nut to the 12th string and then from the 12th string to the bridge. You may need to do an intonation after a string change!
Did you mean will your guitar require a new set-up, as in aligning the neck and adjusting string height, etc.? Chances are, yes, it will require a new set up. Assuming you took the strings, pups, bridge/tail, and everything else off to do the actual relicing of the guitar's finish, you will need to set it all back up when you do the reinstall.
One thing about bolt-on necks is that when you take the neck off you may find shims have been placed where the neck is bolted to the body. So you will need to figure out what you need to do to set the neck back on to the body to get it 'true'.
If you are not sure what you are doing, learn first! Then take the guitar apart. Or, trash a cheap guitar first, then work on the better ones!
Whatever you decide, good luck!