As the second /e/ build for the Fairphone 3 is out, I took the opportunity to check whether my theoretical backup and restore procedure with an unlocked bootloader works with /e/ in practice, too. (It did work with the stock Fairphone OS, but better safe than sorry.)
- Made sure I kept the install file for the initial 20200428 build.
- Made a copy of the whole Internal Storage (because).
- Made a TWRP backup of my installation of the 20200428 build, including the data partition.
- Updated /e/ successfully to the 20200514 build.
Had a look which slot was active (Fairphone 3 is an A/B device), just to be sure to only mess up one slot if in doubt 
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- Installed the /e/ 20200428 build to the same slot where the 20200514 build was installed before, including wiping the data partition according to the install instructions.
- Booted /e/ and set up the screen lock (= the decryption method) the same way it was before.
- Restored the data partition with TWRP.
- Copied the whole Internal Storage back to the phone.
This worked, the 20200428 build was back with all my stuff as if nothing happened.
The only cleanup left to do was to set my own custom ringtone again.
The ringtone gets set back to a fallback generic one by the OS because the OS is up and running earlier than when my custom ringtone comes back later with the Internal Storage copy.
- Updated successfully to the 20200514 build again, so this restore didn’t break OTA updates.
(If somebody finds out how to simply restore everything including the OS out of a TWRP backup, please do tell. I ran into a bootloop trying this, just as I did with the stock OS.)