If I change from a 9-(42) set of strings to a 9-(46)???

thanks!

It's possible. Even changing manufacturers with the same gauge strings may change the intonation.

Every time you change strings you should check your intonation. It's very easy to do and only takes a few minutes with an electronic tuner.

yes

You should check it. And maybe your truss rod for proper neck bow .

Look first what is your action and after you change for the new set of strings if action is high , this mean neck need a truss rod adjustment.

ok, I'm getting a guitar soon, and I wanted to stick with the factory settings but I want to test if I prefer 9-42 or 9-46 fender strings, aswell as testing many types and brands of strings I've never tried before, Fender nickels, DRs GHSs Daddario's on a strat, Dunlops maybe. Im changing the plastics anyway, but I'm just afraid of tampering the settings and lossing the factory settings! But if you guys say it's easy then there's not much to worry right?

You just have to follow the proper Fender set-up . For truss rod allen bolt , be sure to use the correct ( tight ) allen wrench. Many times the Fender allen wrench is too loose and can dammage the truss rod allen bolt / nut .