I'm having a difficult time understand what you need and what you have done. Can you elaborate on that? 

Mostly sorted now, my problem was I needed to change the type of two of the properties in my Variant model, obviously in Commerce this blows up and requires some manual deletion.

So I followed http://world.episerver.com/documentation/developer-guides/commerce/catalogs/catalog-content/

1. I remove my meta class with the meta field for the properies affected
2. I restarted IIS so that the delete button was shown on the meta fields affected (It wouldn't show unless I restarted)
3. I removed the two properties that had changed (The type dropdown was locked and I couldn't change them without deleting them)

At that point rebuilding did not make the meta classes come back at all, I had to go in to the catalog manager in the CMS and create a type of this meta class for these to regenerate. Tho it's quite disspointing that all the views and bits in the database just get left behind orphaned.

After working with Episerver for such a long time now from 7 up to 10 I've gotten used to the ease of model building and in commerce it's just really awkward.