No, I didn't use any fork, but used the master branch of this repository which is version 2.1:
https://github.com/geany/geany/blob/master/meson.build#L3
The problem disappeared after I switched back to 2.0 _and_ added following to my `~/.ssh/config`:
``` Host * ... ServerAliveCountMax 5 ServerAliveInterval 15 TCPKeepAlive yes ```
I've been now heavily using it and while there was a small freeze from time to time, no crashes or anything which caused Geany to become unresponsive or lose all its data as before.