From time to time, a software upgrade is is needed. A upgrade - in contrast to an update - is a more invasive way to install a new version: Everything is deleted and installed from ground up. This is required e.g. when you want to upgrade from LineageOS 17 to LineageOS 18, like I recently did for a Fairphone 2 phone.
Here are the upgrade procedures for Upgrade LineageOS on FP2. There it is described as step five:
Wipe your data partition (this is usually named “Wipe”, or “Format”)
This basically means that all your apps and their data is deleted… in other words: factory reset.
So, it’s wise to do a full backup before you try to upgrade, so that you can go back to a known state. This is possible using TWRP, the TeamWin Recovery Project. With that you can backup all partitions and restore them again. This is described e.g. in How to Back Up and Restore Your Android Phone with TWRP.
The backup is stored e.g. on the internal storage, from which you can copy the images to your notebook. TWRP supports MTP, so you can directly access the internal storage while recovery is running.
In addition to the partition images, you also should backup your internal storage (or SD card). This is not part of the partition images created by TWRP and this is usually the place where you camera photos are stored (look inside the folder DCIM). Some apps also store here additional data there.
With this backup, you can really go back completely. TWRP can restore the partitions and you can restore the internal storage yourself and then it is as if nothing changed.
Note: In order to use TWRP, you have to have your phone’s bootloader already unlocked. If you were using LineageOS before, this is already the case. Otherwise: You need to unlock your bootloader first. The procedure is device dependent, but it usually involves that all data is deleted… So, you can’t to such a full complete backup in that case.
Now you can upgrade your phone knowing that you can go back in case you’ve forgotten to backup anything. After upgrading LineageOS you’ll need to reinstall all the apps you want. If you’ve connected your android to your google account, a backup of all the apps (and some of the configuration data) is performed regularly and that helps you in reinstalling everything. This is described on Back up or restore data on your Android device. The backup can also be triggered manually and this should be done just before you shutdown the old LineageOS version the last time. The backup includes contacts, SMS/MMS, wifi settings, etc. You can find this backup usually under Settings / System / Enhanced / Backup.
But there are also other apps, especially messenger apps. When you reinstall these apps, you need to register again and often you loose all your chat messages. Sometimes you even loose your contacts (e.g. if a new account is created for you in the app upon registering).
Here is a small list of apps, and what to do:
Signal: you need to make sure you know your PIN, so that you can register again. In order to keep your chat messages, you’ll need to backup them manually in the app, see Signal auf neues Handy umziehen: Eine Anleitung. The backup is stored on the internal storage (so copy it via MTP) and it is encrypted. You’ll have to write down the encryption key phrase. When you reinstall Signal, you can select to restore the backup before you register again.
Telegram: no special backup is needed. Everything is stored in the cloud anyways and it is automatically restored if you use the same phone number. Note - if you switch the phone number at the same time, this is more difficult.
Threema: You need to do a manual backup of the data. If you just use the “Threema Safe”, only your identity is backed up, but no messages. See I have a new phone - how do I transfer my data?. The backup is stored on the internal storage (so copy it via MTP). Make sure to include media files in the backup. The backup is protected by a password you choose.
Viber: Viber supports a backup in Google Drive. Make sure to include media files like photos and videos. Manually trigger the backup to make sure, it’s up to date.
WhatsApp: That similar to Viber. WhatsApp supports a automatic backup in Google Drive.
For some other apps, you’ll neeed to make sure, you know your password / credentials to be able to reconfigure and connect them.
The corona warn app e.g. doesn’t support a backup of the exposure data, see this feature request: Backup exposure history to transfer to new/reseted phone. But not even the vaccination certificates are backed up. So you need to import them again, after the app is reinstalled.
Also it is useful, if you create screenshots of the start screens in order to restore it like it was before.