@rmackay9 This is what I was talking about when i first head about someone talking about there being a 4-day limit. that was when I went looking and found that blog post, I assumed they were related. Sorry for the confusion, that blog post was the only documentation i could find on any kind of long term time issue with ardupilot that had a fix, and when I seen the fix was for Linux I thought that it was only fixed on linux not that it was a linux only problem.
this is the part from the locarb blog, its the only other documentation I can find of the issues im experiencing.
Navigation (Pixhawk 2.4.8)
LOCARB navigation is based on open source Ardupilot software with a Pixhawk 2.4.8 flight controller as its hardware base. The pixhawk controls the GPS, compass, telemetry, IMU, and rudder servo. Being an Ardupilot based navigation system, freely available ground control software (such as Mission Planner) makes for creating way-points “simple,” and allows for easy two-way communication with the autopilot.
If I was to build another boat, I would most definitely not use this platform again. It introduces too many unknowns into the navigation process, has too many frivolous settings required to get it operating correctly, requires another hard to understand Arduino library to control it, and is unreliable.
When powered on for 1 week durations with no reset, the autopilot fails to respond to new waypoint commands without having to be rebooted first. It also loses control of the rudder randomly and requires a power cycle to get the rudder operational again. It seems to lose track of the heading over time, and just introduces too many unknowns in the way the boat navigates because it is generally unstable. I just couldn’t trust it to do what it was told so was left second guessing why the boat was behaving as it did (was it the wind/currents pushing the boat or the autopilot?). With the limited amount of data available during the journey, it was problematic trying to troubleshoot. I say stay away from these solutions.
I would usually find it unresponsive since i didnt keep mission planner connected but would check it every day. most of the time it wouldnt connect or when i did connect there would be just weird telemetry coming from it like it would be doing 400meter circles at high speed despite it being parked in the garden, or the hud was doing backfips every few seconds.