Problem/Motivation
If the source ceases to have data , this is never reflected in the destination. There are two problems (at least), this patch attacks the field level in the content entity base, config entities and raw config entities are also broken but probably needs to be different issue and less severe because this only comes up in reruns, the migrate_drupal path does not really support reruns. And then there is the case when a whole row / entity disappears but that is an entirely different issue.
Proposed resolution
Unset outdated data.
Remaining tasks
Test this. Think it through.