Seems like it is still crashing, yes. I'm using the game's built-in update rather than re-downloading the .exe though. Might not be properly overwriting something?
You should use the itch.io app for updates or re-downloading it from the website manually. The built-in updater was giving a lot of issues and we removed it from the game.
The totem for it is coloured in, at least. Not sure if that means the game thinks I've beaten it or that shows I've just found the boss.
Coloured seems like you found where it is, when you destroy the monster you should see the totem broken on the menu as well
As for the missing totem, it was in a folder flagged so it'd only show up if "Hide protected operating system files (Recommended)" is unchecked. That'd explain why it wouldn't show up in Explorer searches.
We will try to avoid creating totems in those kind of folders!