(note: I'm just a guy taking a flyby look at bugs)
The following script is used to generate the key: /usr/share/synergy/gen_ssl_pem.sh
Fixing that script is easy enough, but that is only the start of fixing the issue.
Firstly grepping the source finds a couple of other places where it seems to be choosing 1024 bit res/openssl/synergy.conf:default_bits = 1024 # Size of keys src/gui/src/SslCertificate.cpp: arguments.append("rsa:1024"); Again fixing those should be easy enough. The final bit though is warning upgrading users, it seems these are manually set long term keys, so merely updating the generation script will not get the old keys out of service.