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- Extract the TXTR you want to replace (and TXMT if you want to replace something in the material)
- Put them in a new file
- Extract the texture file, recolor it
- When importing it back, use PNG format, and DXT3 or 5 (this updates all sizes automatically). Click "commit".
- Save the file.
- Put in your game.
Is there anything other than this you've been doing, maybe?
If this is what you've been doing, can you upload the file you're currently working with, so we can take a look at it?