Ender IO introduces a tinker's Construct material for vibrant alloy, and the direct tinker's construct attribute. Tools with vibrant alloy handle or extra parts get direct, but it can also be added as a modifier using a vibrant alloy large plate. Unfortunately, tools with large plates as a part, such as hammers, can't have this modifier applied because the large plate in the tool will get replaced instead.
Replacing the existing large plate in a tool takes precedence over applying the direct modifier so tools with large plates can't get it.
Applying the direct modifier should take precedence, or the recipe shouldn't conflict.
As far as I am aware this is not an issue on our end, but rather with the way swapping parts works with tinkers.
Tinkers used to have this problem with Iguana Tinkers Tweaks' tool swapping when using the obsidian plate for the reinforced modifier. Perhaps a similar item might help?
One of the last TiC updates fixed a bug which causes a similar issue. Parts could not be replaced if they have no traits. Maybe this could help you.
This got overlooked sorry
https://github.com/SleepyTrousers/EnderIO/commit/e09e03e735351a73e24ac79c58fd43b92a00c771
Edit wrong link lol
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As far as I am aware this is not an issue on our end, but rather with the way swapping parts works with tinkers.