The way I see it working is:

1. Have all the major clients and SDKs support encryption and decryption for both NIP-04 and NIP-44 for some time but have NIP-44 be the default for encryption.
2. Clients can allow users to migrate their signed NIP-04 encrypted events by decrypting them and creating new ones with identical content but encrypted with NIP-44.
3. Once most people stop creating new NIP-04 encrypted events, remove support for encrypting in NIP-04 and support only decrypting NIP-04 moving forward. NIP-44 becomes the only way to encrypt events.