I'll post what has worked for me, just for the case someone were using the same versions and facing similar issue.

I switched the projects to .NET 8, and upgraded OpenIddict via versions 4.x and 5.x to version 6.0.0, using OpenIddict's author's instructions:

• https://documentation.openiddict.com/guides/migration/30-to-40
• https://documentation.openiddict.com/guides/migration/40-to-50
• https://documentation.openiddict.com/guides/migration/50-to-60

All the steps were smooth and easy. Once done, the custom claims are back, all seem to be working fine.