It sounds like you’re using Cubasis to record MIDI it receives from your Juno. It’s a workflow problem, not really a Cubasis one, it would happen with any DAW.
You’re sending MIDI to Cubasis. MIDI is note information only, it doesn’t carry any audio, that’s why you can’t freeze it, there’s no audio in there to freeze!
It sounds like you’re using a bunch of different tracks from the Juno, so what you must do is create an audio track for each MIDI track (if you want to keep them independent), and then record all the tracks as audio into Cubasis, because at the moment you have no audio at all in Cubasis, just note information.
You can keep the MIDI tracks as a backup (just mute them), in case you want to make adjustments later on.
If you were only using one track out of the Juno, you could set it up so it’s still live, without recording the audio.
You can have a MIDI track sequencing your Juno, and then an audio track receiving the audio back from the Juno, then you could apply effects to that track, without the need for recording as audio, until you’re done with it.