Actually, no.
If you have checkpoints (from using the "cheat" or any other variation at the beginning of the game, or the checkpoint mod), they actually remember whatever choices you make after the checkpoint when you load back to them. This is why they can occasionally cause some issues, although g28 has done some good work making it automatically lock you out from redoing actions that might have conflicting choices in them that could actually break the game.
What I do suggest, though, is making an actual separate save before making a checkpoint, and then doing all the checkpoint shenanigans you want to do, because it is possible, at least on one or two occasions, as far as I remember, to end up soft locking yourself using checkpoints on one of the earlier days during the "free time" section, by running out of actions. Not sure if that has been fixed since I did that to myself, though.
Also be aware that some things may end up happening that you didn't necessarily want by doing all the things with checkpoints, that you could have avoided by not doing said things, and you still may cause things to break in weird ways, like having characters randomly switch to their bimboified/youngified model even if you never used that light on them, which can only be resolved by using the dev console, as I explained in an earlier post a couple of pages back.
Checkpoints can definitely be used to do a lot of fun things, though, and I certainly think it's worth exploring them if you want to see a bunch of things, but they can actually lock you out of seeing some things, strangely enough, so it's also worth doing playthroughs without them afterwards, or even only using them sparingly.
