V11 upgrade from v10 rewrites the names of my custom doctype that has autoname set to prompt

I am not sure if this is a feature or a bug.
I have custom app with a custom doctype with auto name set to Prompt.
The specific naming of my doctype is important which is why I set it to prompt.
When I run the upgrade it renames all of my entries.

I see these scripts run during the update
Executing erpnext.patches.v11_0.refactor_autoname_naming
Executing erpnext.patches.v11_0.rename_mycustomdoc_with_naming_series #04-06-2018 in www.mycustomapp.com (1bd3e0294da19198)

mycustomdoc has all of the names changed to some series.
I would like to upgrade but I need the names to stay the same
How do I prevent this. The names have meaning and the new series does not.