2)
- Using console commands gave myself BGWhetstone
- Entered BGliving_wall event
- Chose "transform"
- BGwhetstone can't be clicked (good)
- Opened map
- Clicked BGwhetstone
- Upgraded strike and and another attack as intended
- The event finished without transforming anything!
Seems like opening map at a wrong time messes up a lot of stuff

Note that this isn't actually the bug I reported previously, but rather similar enough issue

3)
I have found the log from the day that my save file got scrambled and read through it. It seems that boss room had nothing to do with the save file corruption, it was corrupted the moment I started the run. Most likely explanation? I had an iron clad save file going from long ago and it wasn't recognized as one during the creation, BUT ended being part of the new save file, kind of adding to it during the silent run. It was probably just a one time bug caused by how differently the data is saved between old version and current.

Here's the file relevant parts of the log:

10:21:34.419 INFO BoardGame.BoardGame> 1-BGWhirlwind 2-BGShrug It Off 3-BGTrue Grit 4-BGWild Strike 5-BGIron Wave 6-BGTrue Grit 7-BGCleave 8-BGAnger 9-BGBattle Trance 10-BGHeadbutt 11-BoardGame:GoldenTicket_R 12-BGSecond Wind 13-BGDark Embrace 14-BGEntrench 15-BGTwin Strike 16-BGFeel No Pain 17-BGCarnage 18-BGWild Strike 19-BGHeavy Blade 20-BGShockwave 21-BGFire Breathing 22-BGSeeing Red 23-BGBody Slam 24-BGSever Soul 25-BGFlex 26-BGDisarm 27-BGWarcry 28-BGShrug It Off 29-BGCleave 30-BGIron Wave 31-BGClash 32-BGBurning Pact 33-BGBlood for Blood 34-BGHeavy Blade 35-BGTwin Strike 36-BGWarcry 37-BGHavoc 38-BGHavoc 39-BGAnger 40-BGSentinel 41-BGPommel Strike 42-BGCombust 43-BGPerfected Strike 44-BGEvolve 45-BGBody Slam 46-BGRampage 47-BoardGame:GoldenTicket_R 48-BGFlex 49-BGClothesline 50-BGFlame Barrier 51-BGClothesline 52-BGGhostly Armor 53-BGSpot Weakness 54-BGRage 55-BGRupture 56-BGPommel Strike 57-BGSeeing Red 58-BGInflame 59-BGMetallicize 60-BGPower Through
10:21:34.424 INFO saveAndContinue.SaveFile> Next Room: com.megacrit.cardcrawl.neow.NeowRoom
10:21:34.434 DEBUG helpers.AsyncSaver> Enqueue: qsize=0 file=saves\BG_MULTICHARACTER.autosave
10:21:34.434 DEBUG helpers.FileSaver> Dequeue: qsize=0 file=saves\BG_MULTICHARACTER.autosave
10:21:34.434 DEBUG helpers.File> Attempting to save file=D:\Gry\Steam\steamapps\common\SlayTheSpire\saves\BG_MULTICHARACTER.autosave
10:21:34.473 DEBUG helpers.File> Successfully saved file=D:\Gry\Steam\steamapps\common\SlayTheSpire\saves\BG_MULTICHARACTER.autosave
10:21:37.422 INFO audio.MainMusic> Disposing MainMusic: MENU
10:21:39.768 INFO BoardGame.BoardGame> getStartingRelics: BoardGame:BGTheDieRelic BoardGame:BurningBlood
10:21:39.769 INFO basemod.BaseMod> postCreateStartingRelics for: BG_SILENT
10:21:39.769 INFO basemod.BaseMod> postCreateStartingRelics adding [ BoardGame:BGTheDieRelic BGRing of the Snake BoardGame:BGShivs ]
10:21:39.772 INFO BoardGame.BoardGame> getStartingRelics: BoardGame:BGTheDieRelic BoardGame:BurningBlood

Notice how it lists a mix of Ironclad and Silent cards/relics.

I've tried to play five runs and have encountered the first bug every time at some point. I haven't gotten past act 2. I've played as Silent and Watcher. Every time I've died, it's been through block, though I haven't experimented to see it if happens without block, since it seems random when it happens.

The mods I was using:
BaseMod
Minty Spire
Quick Restart
StSLib
Bestiary
Colored Map
Highlight Path
InfoMod
Achievement Enabler
Permanent Neow
Deck tracker
Fast Multi-Cast
Super Fast Mode

With 1, I experienced something similar that I think was due to another mod I had (Quick Restart). If I used the mod abilities to either restart a fight or go straight to another run after dying, I think that character health didn't get properly reset? But things seemed to work normally if I either did regular save/quit to restart a fight or went back to the title screen after losing a run before starting another run.

Based on the above post, I disabled Quick Restart and managed to play a full run from start to finish.

For me it was the same with problem #1. And disabling the quick restart mod was my solution (before reading this).

Trivia time! Behind the scenes, the game is running multiple characters simultaneously in the naive hope that I'd eventually get to use them to implement proper multiplayer. Something about Quick Restart causes the enemies to start attacking one of the wrong player characters hidden "behind the curtain" instead of the one you see on screen.