Hopefully someone can shed some light on this. I just finished a Storymode run where, upon getting the frog kill, the frog npc was missing, the post-fight cutscene never played, the "Truths" never showed up and, when exiting, the heaven door disappeared. I just doubled checked my saves and, every single file was empty, so I'm not sure if my run is now invalid. Tried digging around other places for an answer, but couldn't seem to find anything. I'm playing on the official Speedrun patch through steam.

Hiya,

I believe the 1.0.1 version of the game has some issues with the pacifist run. Definitely recommend trying to grab version 1.0.11 using DepotDownloader or similar and trying that out. It has way less issues but still has the relevant stuff for any%.

Edit: Just realised that the depot downloader guide isn't on this site. Adding it now.

Hopefully posting this will save others some time. If you need a copy of v1.011 using DepotDownloader, the proper manifest id is: 9004346172252630095