alt Hacker NewsMatrix published a proof of concept a few years ago of an alternative transport layer designed to work over connections with a few hundred bits per second, and massive packet loss, while still providing E2EE:
https://matrix.org/blog/2019/03/12/breaking-the-100bps-barri...
Without knowing that much about this area, i think https://mosh.org/ is a traditional choice if you need encrypted communication in a high packet loss environment.