When repairing Leather Armor that has been dyed it will always produce a different Leather Armor piece. This piece of armor will have the correct amount of damage, but will always be uncolored. This will even happen when using armor with precisely the same color or between a dyed and an uncolored piece. This can be a problem when using nonrenewable colors such as blue (Lapis Lazuli). The Anvil will preserve the enchantment and name as usual, but it will come out uncolored.
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Cannot reproduce, see attached screenshot. Are you putting the colored armor in the first or second anvil slot (order matters, the item in the first slot is the one being repaired).
Tails: It's hard to see, but he said this occurred on the anvil.
Use an anvil if you want to preserve the color.