Reading the other comments, I see a lot of people advocating for just skipping content. That's good, as long as the skip is actually canon. If you skip content and it really didn't happen, that's fine. If you only skip the scene and the skipped events remain canon, it's pointless to even bother.
This means that there should be a visible choice and at least a minimum of optional narration that ties the parts before and after the skip together, to establish a new canon where the skipped scene really didn't happen. Future events should acknowledge those events only if they happened, not if they were skipped.
Alternative sex scenes sound great at first [edit to clarify: they aren't], since it looks like you're giving the player something to make up for the missed content. But now you have two paths where one will always be missed, and that FOMO does not feel good, particularly in a harem game. I mean, harem games are specifically targeted at completionist players who don't want to drop one route for another. [Edit to clarify: Optional paths are great, forced choice between alternative paths is bad.]
I would wholeheartedly agree with having the skipped content in the gallery, so you can see it as a kind of fragment from that alternative timeline. If the scene contains important dialogue, make sure to include it.
[Edited for clarity.]