For anyone experiencing this issue while running an app on Android 11 (API 30, even when targeting API 29 or lower with the build), it is confirmed to be intended behavior as Android OS no longer unregisters geofences when location services are turned off.
However you still cannot register geofences while the location services are off and thus must check their availability and prompt the user to turn them on whenever registering new ones is required. The previously registered ones do not need re-registering.
No relevant information has been given as to how this can happen on devices running Android 10 or older, which has also been reported by some developers. But it seems safe to assume the change was introduced earlier at least in some versions of Android OS (depending on device manufacturers). It would be very helpful if the original question mentioned whether this issue was on just some APIs or not, but I imagine due to its age it wasn't concerning Android 11. If anybody who has encountered this issue on lower APIs could test if their old geofences remained registered and usable, I'd gladly update the answer accordingly.
Source:
https://issuetracker.google.com/issues/143967408
UPDATE:
As mentioned by Stephen Ruda, it appears that it's not dependent on Android OS version, but on Google Play Services version. Which makes this behavior completely unpredictable.