Here's how I addressed the automap palette bug:
Oh I didn't know you tackled this issue already. You NOP (x3) the STA $6C00 at 0x19D99, correct?
I added the 3 NOPs in place of that STA, and sadly it's still not working for me.
As soon as I start a game and Pause to check the Subscreen, the Subscreen starts flickering like crazy.
If I manually add $00 to $6C00, then it stops doing that.
I tried with standalone Automap, and it seems to work there, but for some reason that solution doesn't seem to be working with Redux :/
I also tried disabling all the other ASM files, except Automap, and that seems to work, but as soon as I active either the Arrows/Rupees ASM files, the flickering returns.
I will see what can be the issue here.
I went ahead and took a peek at the Automap source released by Snarfblam some years ago, and I rewrote the entirety of the automap.asm file on my end to match his notes and definitions. I just did this to cleanup the file, though, that wasn't done to fix the issue or anthing.
But aside from the cleanup, I think I found a possible solution for this issue, but still haven't pinpointed how to properly implement it, as I need to find 6 free bytes near $6C00 in RAM.
The RAM Address that's at fault here seems to be $6C00.
I did some slight research, and apparently the section before and after $6C00 gets loaded with Overworld/Dungeon data found at bank 6. From the slight section of data around $6C00, I think I found a section that doesn't seem to be used by either Overworld nor Dungeon data, which I could repurpose for the Automap Tile Flag ($6C00).
From my quick tests between dungeons, it seems the range from $6BE1-$6BF9 goes unused in vanilla Zelda 1, but this range seems to be used by some PPU transfers with Automap itself, so I need to find 6 bytes of unused RAM around that section to be able to change Automap's code (and the STA $6C00) to work properly, without it clashing with either Overworld data or Dungeon data.
I went for RAM Address $6CB4 for the Tile Flag (and its 6 bytes).
I noticed $6CB4 goes right after the end of a routine in the Rupee ASM, around $0D bytes of dummy $FF bytes, so that seems to be a good place to put it at the moment. Will check if something borks or not with that later on.
I also found the culprit of the issue with the Subscreen map for Level 6 not showing up.
Seems to be this code precisely that makes it screw up:
org $992D // 0x1993D
db $10 // Originally $F1 ($10)
Such a small change, and it seems to be what borks up the map for Level 6 specifically.
All others are untouched.
I don't know why this value was originally added. I know Bogaa helped me with some stuff in this move_maps.asm file, and this value was added alongside the value to move the dot for the overworld automap to the right of the screen.
That specific change at 0x1993D seems to be modifying the table for the Drawn Map Data for Level 6. It changed the $F1 there for $10 for some reason. Dunno why.
I'll remove that code in the meanwhile, as I have confirmed and verified it does nothing but bork the map for Level 6, I'll still check with Bogaa to be absolutely sure, though.
In the meanwhile, all the fixes and revamped code for Automap has been updated in the GitHub repo.
The latest commit should also have the fixes for both the Palette bug with Automap, and the Dungeon 6 Map not having certain tiles appearing.