Edit: Ok, so you unlocked your bootloader and used TWRP. I’ll leave my post here anyway for other passers-by.
The telling bits are these here …
I got these messages, too, simply from using TWRP for the Fairphone 3.
It’s important to use the latest TWRP version and only let it mount system as read-only.
Without that setting even just installing something with TWRP without you explicitly mounting system before will mount the system partition read-write nonetheless and thus break OTA updates.
With an unlocked bootloader you can boot TWRP and restore the stock OS (currently A.0105 or A.0110).
Or you can flash stock A.0111 with fastboot onto the active slot.
Both methods should leave your data and the Apps intact.