There’s some information on how to upgrade in the official release post from back in early 2022.
For some additional clarity:
- BlueOS is software which acts as an operating system wrapper for the onboard computer (which is a Raspberry Pi 4B on our latest vehicles).
- The flight controller board is separate hardware, which typically runs an autopilot firmware (e.g. ArduSub).
- There’s a diagram here that may help visualise the differences
Depending on when you bought / set up your ROV it may already have BlueOS installed, or our older Companion Software. If you’re not sure you should be able to find out from the vehicle’s web interface, which for Companion is at port 2770 (e.g. http://192.168.2.2:2770). BlueOS has a few different ways you can connect.
If your vehicle has a Navigator flight controller board then you’re definitely on BlueOS, and if you have a Pixhawk and you haven’t upgraded the vehicle to BlueOS then it’s most likely running Companion.
If this is just the standard temperature measurement(s) from a sensor that’s connected to the flight controller board (e.g. a Bar30, Bar100, or Celsius) then that’s mostly unrelated to the onboard computer software.
If you have some kind of custom water temperature sensor that you’ve integrated (which seems unlikely) then whether it’s affected by the onboard computer software will depend on how you’ve done that integration.
Cockpit does also generate subtitle files with its video recordings, and it provides much more control for that than QGroundControl 
It depends on the cause of the issue.
If Cockpit fails then that has no impact on QGC, but if the autopilot firmware (e.g. ArduSub) or onboard computer software (BlueOS) fail somehow then that will typically impact both QGC and Cockpit equally.