That does seem odd - did you do one ending without seeing all the chimera scenes, then go back and do the remainder you missed + the Yaldukra scene before doing the second ending, but still had him show up in the first? I'll have to look into that further as a potential issue if that's the case - thanks for your help.
Either way, it's great to hear that you enjoyed your time with the game.
I did both the upstream and downstream ending first without seeing the final chimera scene. I don't remember seeing Yaldukra in upstream, but I distinctly remember the whole "I'm guessing that you had something to do with this," conversation in downstream. I also remember being really confused when he spoke about how his tattoo reacted to... something that sounded likely sexual in the Side B content.
Then, I went back and finished the chimera scenes before going downstream again, and I didn't initiate any conversations with Yaldukra because I'd already seen them.
The extra chimera scene was the only one that I hadn't been through by the first go-round, though, so maybe it had something to do with that? I also remember running into some chimera in that well-lit area right nearest to the extra scene, but I never caught up with them, nor could I get them to reappear. My guess would be either THAT... or that I at some point played the game in a fugue state and had unlocked all of the chimera scenes all along. (Although the latter wouldn't explain how I went back and saw the scene after I re-loaded my save; I only saved once before the point of no return.)
Sorry if I'm not much help with identifying the issue. I haven't noticed that anyone else has claimed the same, fortunately, so maybe it's just some sort of fluke with how I handled the files.
Same exact thing is happening to me and I'm not even done yet. I saw the scene with Greenhouse, I walked past the save point and it said something was unfinished, so i walked back to a random area, the usual glitchy chimera flew at me (it looked like Patricia) and.. nothing happened - then the bridge would let me pass without talking about being 'unfinished'. Then, downstream, Yaldukra says I saved him somehow. I'm thinking something bugged out and a scene was just.. skipped?
Reloading and trying my best to start the fight with it changed pretty much nothing, exact same problem over and over.
