Managed to solve it - posting here for future ref if anyone has the same issue!
This is a known bug with electrs. The only way I know to fix this is resetting electrs, but please note that this means some apps won’t work and some wallets won’t connect during the ~8h indexing time.
sudo systemctl stop umbrel-startup && sudo rm -rf ~/umbrel/electrs/db/mainnet && sudo systemctl start umbrel-startup
This command via SSH will reset electrs
You can try rebooting and waiting a few hours, maybe it’ll compact the DB automatically