Hum.. do you see your bookmarks in anyother client? Amethyst would have migrated it from NIP-04 to NIP-44 automatically. Then other clients might not be able to see it anymore. If those other clients than try to save it, it would most likely delete your older list and start with a new one.

I can write my filters here, but I think that I've lost it all, ah another thing, in the latest version the communities kind 10004 was empty too. I see that the amethyst prefer to add the communities in the kind 3 than 10004. I think that the kind 10004 is for joined and the 3 is for following, what do you think about that?

Ah, I'm working in the @npub19wjh...t7m8 client and I use the kind 10004 to list the joined communities...

Nice, make sure to decrypt using both NIP-04 and NIP-44 (you can search for =iv in the ciphertext to know if it is NIP-04, if you cannot find it, give it to the nip44 decrypt method)

Version 1.00.0 migrated kind 3 to kind 10004, but with nip44

Encrypted communities are the best approach to follow now? What's your vision about the public communities? I think it could be good to see what are the communities of an user.

Each client can choose their own. Amethyst will show both, but always encrypt the ones followed in Amethyst

Then we could consider the communities in the tags could be the public ones.

Yes, the communities that are in the tags are public, the ones encrypted in the .content are private follows.