Ok, I found the Troubleshooting guide on the Knowledge Base and managed to interrupt the automatic load process by repeatedly pressing the Bela button very quick.
This is what I got on the console when I was able to access it on the IDE:
-- Logs begin at Thu 2016-11-03 17:16:43 UTC. --
Nov 03 17:18:39 bela stdbuf[1854]: Button pressed, quitting
Nov 03 17:18:39 bela stdbuf[1854]: Underrun detected: 1 blocks dropped
Nov 03 17:18:40 bela stdbuf[1854]: make: warning: Clock skew detected. Your build may be incomplete.
Nov 03 17:18:40 bela stdbuf[1854]: make: Leaving directory '/root/Bela'
Nov 03 17:18:40 bela systemd[1]: bela_startup.service: Service hold-off time over, scheduling restart.
Nov 03 17:18:40 bela systemd[1]: Stopped Run Bela at boot.
Nov 03 17:18:40 bela systemd[1]: bela_startup.service: Start request repeated too quickly.
Nov 03 17:18:40 bela systemd[1]: Failed to start Run Bela at boot.
Nov 03 17:18:40 bela systemd[1]: bela_startup.service: Unit entered failed state.
Nov 03 17:18:40 bela systemd[1]: bela_startup.service: Failed with result 'start-limit-hit'.
I SSH'd into the bela and manually deleted the _main.pd file for my project, and then set the "run project on boot" to "none." I think I'll leave it like that until the patch is foolproof!
Now let's figure out why the project is crashing, hm!
Update: I added two bob~ filters which brought the patch's CPU usage over the top. Now looking for more efficient filters.