When an update is run and an external source is not present, the cleanup process removes all the entities from that source. My proposal is similar to how Kodi handles this. In Kodi when you run Clean Database and it finds that an entire source is missing, it asks what you want to do, keep the data or remove all of the data from that source. This prevents having to add all of the data again when the external source is back.
In TMM, this is a long process if you have a large library as it needs to collect media information. I know that the user has the option to prevent this, by either running the update on selected sources only or making sure the external source is there prior to running, but this can be easily forgotten.
Summary- Feature request to have a verification question when a source from the list is missing completely, do you want to remove all the data from that source, or ignore and leave as is.