This may be the issue. Packages installed through Flathub (known as flatpaks) have restricted permissions by default so that they cannot access the filesystem freely. If going with the preinstalled version of Evolution is not an option (which would mean downgrading to 3.4.4), then I suggest you install Flatseal from the Software Store and give the necessary permissions to Evolution:
Add a new entry as shown; xdg-run is short for /run/user/<user_id> which should grant permission to that whole directory and everything underneath it.
If this doesn't work you may need to grant permissions to ~Documents/protokol 50 as well.