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I have the same issue, I am using KeepassXC, and I unlock the database using Yubikey Challenge-Response mechanism. If I can help in any way let me know.
If you can figure out how to do this in PyKeePass (pass in decrypt=False when opening database, then some stuff needs to happen with the masterseed and python-fido2), we can look at making a pykeepass-fido2 package which would add support for fido2 keys.
It would be neat to use this CLI tool, but my file is protecter using a YubiKey.
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