Sorry for another bug report so soon, but I just restarted the game after maxing everything(?) out, and upon restarting it, I've found that I have the same amount of health that I did in my previous playthrough. Not as in I'm missing health, but in that I have more than I should. Progressing further I've found that the dialogue didn't reset either, upon talking to Tunnel Greg he gave the "My mind's folded in upon itself" line instead of the usual introductory cutscene. I've also found that (I forgot her name sorry) the "Sludge Wilds" woman and her camp didn't spawn in. Tara's dialogue did reset, same for all of the other Deep Town residents. I didn't retain any of the upgrades, so that was fine. In summary I think the only problems were the health, Tunnel Greg's dialogue, and the "Sludge Wilds" woman. Also in the previous playthrough, I fell into the sludge near a sign (not one of the readable ones, it was like a stop sign) and instead of being spawned back to safety above it, I kept spawning in it so that I had to exit the game and respawn at the previous checkpoint. Sorry again for the bug dump, I'm sure you've heard most of these already. Chrome on a cheap Chromebook again, for the platform.

EDIT: Upon restarting the game again, everything's reset.