Iām just saying that there is a flaw in your backup strategy, and this situation revealed it. The backup to the external drive should happen only from the known good state, manually or at least with wide enough interval to be able to stop it if you notice a problem.
The 3-2-1 backup strategy is accepted to be safe and is generally considered as good practice for data that you care about. Itās 3 copies in 2 locations with 1 being offsite.