No, it will not. As long as you have your league’s keepers assigned (MVP/HOF/GOAT Feature) within the Draft Wizard®, the players will automatically appear as crossed off on your cheat sheet when using the Draft Simulator and Draft Assistant.

If you’d prefer to have a cheat sheet that doesn't account for keepers, you can create a cheat sheet from projections and select your imported league in the cheat sheet's league settings. This would prevent your keepers from showing up on the new cheat sheet.