As you can now change your minecraft name, be warned that if you do so, it is likely that you will encounter problems on modded servers if you've already started playing on them. Not all mods have moved to the UID system of referring to players for various reasons (it has problems of its own), meaning they will likely see you as a completely different player if you change your name.
is it the player files on the server that'll be effected or the account logging into FTB or similar launchers?
Some launchers will require you to create a new profile. Thaumcraft stores all its research by player name and Baubles are also stored by player name (same dev) for example.