its not that some scenes were removed.
Its more correct to say, the version 2.xx is a remastered version of the original game, an entirely different coding was used. And with this a good amount of scenes where re-coded, and some "are supposed" to be included in future versions.
In this situation, the game isn't finished yet, so in a future version, at least at some point, the remastered version should include everything version 1 had (unless dev planned to change something, I don't know). And after that new scenes are included to continue the original games plan. Btw there are already new scenes that never existed on version 1, though I am still waiting for scenes that include the leader of cheerleaders lol.
Btw, the dev is still working on this game, right? I feel its taking more time then before to release next versions!