If rooted debugging can be enabled in developer options on your device (i.e. it is a dev build rather than stable) and you have access to a computer (or a Virtual Machine), running Linux, then you can use the Android Backup and Restore Tools project to back up your apps and user data.
It doesn’t backup absolutely everything. In particular account details and passwords, in Account Manager, in Email, and in other apps.
You can export your Email settings and import again after a clean reinstall of /e/OS.
For Call logs, install SMS Import / Export from F-Droid, and backup to external SD.
Backing up your data partition using TWRP backup is also useful, so long as you backup to an external SD card, or copy the backup from internal storage to your PC. TWRP backups from one device can usually be restored to a different device of the same make, model and /e/OS version,
See my post on both (which is quite old, but still mostly valid I think) for more information