Ok, so I think .chr files work like this
(sorry for making it a bit of a long story):
chr files have 9 subfiles. (I can't guarantee this is for all chr files) And the header contains the lengths of the subfiles (32bit integers). The first value is 0x00600000 , it's little endian so flip the bytes and you'll realise this file is 6000 bytes long. That means the first file is at 0x24 (length of header) all and goes all up to 0x6023. (0x6024 is the next file)
This file contains an image stored in tiles.
The second file is what I call a map file, Puyo Puyo had a shitload of these and they can be quite awkward to work with if you don't know what to do with them. (Quick explanation: a map file contains the tile arrangement of an image, that's why I call them map files, because they map the tiles.) HOWEVER: apparently this game (it's Ys I presume?) hardly makes use of this, this game doesn't store its tiles "efficiently". In a tile editor, this file would appear as vertical stripes. I shouldn't talk about this too much, I can explain a lot about them, but it's not so interesting for your case.
The third file is an image again, the 4th a map file, etc. However the 9th file appears to be palette files. I recognize the values 0xFF7F (this is white) and 0xE003 (a yellow, usually used for transparent color), so I'm very sure this contains palettes.
Now back to your original question about editing these: if you want to use tile molester, I'm afraid I can't really say much about it. I'm sure it's capable of editing this particular image file, try to set the offset to 0x24 and make the window 256 pixels wide (32 tiles). Personally my approach would be making my own tile editor (simply because I don't like any tile editor that is around on the internet) and customize it for .chr files, but that I don't have anything to say on that of course
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