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I recommend a fully new setup of the operating system (deleting every partition on the OS drive and beginning from scratch. Simply updating over the existing installation will keep all unnecessary software intact). Doing this will completely clear your registry, so you’ll have to reinstall your games.
Your personal items such as music and photos can be relocated, but game files (including save data) won’t function properly. If you got your games from Origin, uPlay, or Steam, they might help restore the setup by moving the games into a specific folder and adjusting the program paths. You shouldn’t run into problems with the motherboard and W8.1.