1) Make sure everything encrypted got an unencrypted copy.
2) After installing the new version re-encrypt.
From current version, all encrypted files will be handled by future versions. This means that you can always download the latest AutoEncrypt and be sure you can decrypt your files - as long as you have the key. If you don't have the AutoEncrypt document where the session is setup, you may need to specify the version of encryption and compression to use when creating a new session document.
If you want to save encrypted data long term, please copy the AutoEncrypt used to the same place where you have your key. The application is small compared to the key size.