The OpenGApps backup script will still run when you re-flash LineageOS.
You can delete the backup script before dirty flashing Lineage again.
/system/addon.d/70-gapps.sh
You can wipe system before flashing LineageOS again.
TWRP-> Wipe-> Advanced Wipe-> Select System, then Swipe to Wipe.
Think of it like a clean(ish) dirty flash.
Since system was erased, no backup scripts will exist or run.
Userdata will still exist so, apps and data will be the same.
Note:
Both options may cause problems.
If an app updated (the update would be in userdata) and the update is linked to something that is missing in system.
library files, permissions, shared dependency..
Good luck.
Cheers.