if possible a good fix would be to make a list of each used colour, and make a separate texture file for each colour (blockbench has multiple texture files, so you could index the colours for the blocks and make tiles of each used colour and set the textures for the blocks to it when importing, then when exporting back if the block uses an index colour file, it checks the colour of the pixel in the top left and sets that colour for the block) or see if there's a way to add the block colours to blockbench since using just the colours for the cubes leads to a smaller texture file and more details in the model (you can make a spot in the middle of a square glow while the edges stay dark and other stuff)