Update: F-Droid 1.16.3 is now available and prevents the below issue from occuring. After updating your F-Droid to 1.16.3 you can safely update your Android version (e.g.: Android 12 to 13).
We identified a serious bug with F-Droid 1.16 through 1.16.2 when doing an Android version upgrade (e.g.: Android 12 to 13), causing F-Droid to end up in a broken state with no apps available and update checking not working.
We are preparing the release of F-Droid 1.16.3 which prevents this bug from happening. It will be out soon.
Please refrain from updating your Android version until you have updated to F-Droid 1.16.3.
If you are affected by this bug, there are several options to work around it.
Option 1: Delete all app data (Android settings → Apps → F-Droid → Storage and cache → Clear storage). Please note that this means you will lose all your settings and third party repositories.
Option 2: Remove and re-add every single repository inside F-Droid. Please note that disabling and re-enabling repositories is not sufficient.
Option 3: Enable “Force old index format” under F-Droid Settings → Expert mode. This won’t fix the problem immediately, but will make the apps correctly re-appear the next repository update (which may still involve several days of waiting). Please make sure to disable the option again after all your repositories are available again, so that you can keep enjoying faster updates.
We sincerely apologize for any inconvenience caused.
For those interested in the technical details of the bug in question, please check the following link: Fix critical bug that prevents repo updates after Android updates (!1210) · Merge requests · F-Droid / Client · GitLab.