Using --notebook-format SOURCE results in missing notebooks and no errors
Overwriting notebooks was desired as part of a migration.
The --overwrite-notebooks flag was enabled, which produced this feedback:
Overwrite notebooks only supports the SOURCE format. See Rest API docs for details
So then the --notebook-format SOURCE flag was used which resulted in a SUBSTANTIAL amount of notebooks not getting exported, but there were no errors. So there is either an issue with the migration tool or the Workspace API exporting notebooks in the source format.
I'm not sure if this is still an issue, but I recently performed a migration to E2 for my employer and we did not have any data loss. I should note though that using only SOURCE files makes users lose their visualizations and dashboards, which is painful from a user experience standpoint.