Persist changes to /system partition on A/B device (Android 9)

I’m trying to add the [F-Droid Privileged Extension](https://gitlab.com/fdroid/privileged-extension) using the OTA .zip to a [Fairphone 3](https://en.wikipedia.org/wiki/Fairphone_3) on which I’ve [installed /e/ OS](https://doc.e.foundation/devices/FP3/) . I tried modifying the update-binary script because the [mount points assumed in the script don’t quite seem to work on this device](https://gitlab.com/fdroid/privileged-extension/-/issues/69) , but although the files seem to be copied fine to the system partition(s) in recovery mode, when I reboot the phone, all the changes have disappeared. Is there anything else I need to do so that files copied to /dev/block/by-name/system_a or /dev/block/by-name/system_b in recovery mode stay around?