Had to factory reset my router (Beryl 3000AX) because it didn't accept the 4.6.4 upgrade, did a backup first.
After the upgrade all good, restoring settings, reboot, GL UI gone, only LuCI starts.
How can I get the original Ul back AND have my settings applied?
It depends on what you break before.
So you might need to check why the GL GUI does not load anymore. Check the nginx configs.
Actually, I didn't break anything - just saving a completely working config, never did any changes in LuCI or similar and restoring that from 4.6.2. to 4.6.4.
Anyway, following your advice - nginx couldn't bind, the ports were in use by uhttpd. No clue how to proceed here and if it's worth to fix it on console ...
Stopping uhttpd and starting ngnix leads to a 502.
Did you enable AdGuard encrypted DNS by chance?
No, I didn't. It's a rather plain config, I'd say. Just MAC based Wireguard is on. Not much added to this.
I did a fallback to 4.6.2 now after trying a few different approaches to import my config with 4.6.4. Interestingly, the online upgrade from 4.6.2 to 4.6.4 fails again. That was my motivation to do a factory reset.
Which version did the backup (.tar.gz) export from?
May I know when you import the backup in v4.6.4, the GL GUI cannot be accessed, right?
Backup is from 4.6.2.
I tried all combinations of import. Last try was clean uboot flash of 4.6.4, the GL GUI was obviously available but after import it was gone again.
After that I decided for a fallback with uboot. Import of 4.6.2 config into 4.6.2 worked fine.
Would you be fine with sending the backup file via PM to me?
Please beware that there might be personal details in it - which I would be able to see then.
Is there an option to remove the Wireguard config?
Look inside the backup folder and remove /etc/config/wireguard and /etc/config/wireguard_server
Will do but not before tomorrow, maybe Sunday.
Hello, good morning. Something similar happened to me. Being in version 4.6.2 I made a backup of the configuration. I upgraded to version 4.6.4 without keeping the configuration, restored the backup and the Gl-iNet interface disappeared. I went back to 4.6.2 and restored the backup. Then I upgraded to 4.6.4 and kept the settings and everything came back including the Gl-iNet GUI.
Regards
Also maybe not relevant, but for both cases:
Had any of you mounted a usb or storage device to /overlay ?
Especially with ext4 styled partitions you can get into issues quick because it litterly overlays the current partition.
With other words, when you upgrade it doesn't upgrade the packages on the overlayed part but on the nand chip.
But when it boots, it still mounts the old overlay from the external device, thus causing to load incompatible drivers with the mismatched kernel version and then get stuck on boot loop.
this might not be the cause of packages, but maybe the fstab got rolled back wrongly?
Never mount a USB device
Sorry, now I have doubts whether I will ever mount a USB device. I am not 100% sure
Mounting isn't exroot. You can mount devices without any issue 
@xize11 was talking about something more special, called exroot
If the firmware upgrading with keep settings and to the newer version is no problem, that is ok.
In different versions, there are probably some new/old/removed features changes that using backup export/import may break the GL GUI.
(As similar situations also occur with different customized versions of OpenWRT.)
The GL firmware upgrades with keep settings, it will optimize the configuration for compatibility after the upgrade. If backup export/import in the Luci, there is no this kind of optimization.
Could it be OP used the package manager to update luci and that installed its uhttpd dependency?
Waiting for the backup file to test with 
Just sent it ...