Version free variables  - adding configurations

I think the issue is that when you set a variable to version free it removes all the link information to custom properties and stuff. It becomes a standalone variable. If it is on the data card it no longer updates when you check the file in or out. You can also change them without checking out the file first.

If it updated when you checked the file in it would no longer be version free.

You will either need to updated the version free variable manually from the data card or have your dispatch do it somehow.

Version Free variable doesn't have any relation to the custom property in the files as told by Paul Wyndham

it can be updated anytime from client editor license if proper rights are assigned without checking out any files
Now in your case, you want to update that for all newly created configurations and sheets added

In this case,  the file is checked out
What you can do is make sure that on file card update all configurations option is checked

you will need to update once and all of the newly created configuration or sheets added will be updated

make sure to update variable after creating all the configurations/ sheets