It can be really interesting to have choices that show up after a playthrough, you would just need to be careful which ones. It almost reminds me of the Clannad VN needing multiple playthroughs to get something to finally get the “true ending”. You would need to be careful with it… Try something like making it so the player can use prior knowledge of an event (The player gets deja vu or something). It can fall into the trap of “… this is clearly right why wasn’t it here last time?” So you need to give an in story reason as to why the player character suddenly is able to essentially change fate lol. Hell perhaps something on the bad ending could be needed even (not the worst ending I’m pretty sure noone wants to go out of their way to be so cruel in a game that’s really trying to push kindness XD) In that you would need essentially the curveball choice I talked about before… Something where the player is shown to have good intentions but it still backfires. Taking the idea even further, there can be whole hidden story branches (This is getting into the realm of “Oh god why did I write so much?!”) but it is definately a good way of having the player explore the game more, especially if you can set a precident that a bad event could lead to a good one. I guess i’m saying it’s awesome IF you can come up with a good way that fits your story 
Obviously, take my advice with a pinch of salt; you already made an awesome story. If there is anything here that’s useful it’s all yours though!