Check your mappings in your variables to make sure none are duplicated to the same variable.
Checked mappings. They're all only mapped to themselves.
There seems no difference between variables that stay put vs ones that disappear
Attaching screen shot of each
Removed all custom properties from part file templates - user can only enter data via the data card now
Then those variables get pushed into the part file and then onto the drawing.
Seems like something's not right, but that's the workaround for now.