Do you have any content models (classes annotated with [CatalogContentModel]) connected to your meta classes? In that case you need to first remove the fields/properties from those classes, and then delete the meta data fields from the UI.
I managed to solve it by removing item and products and then removing the metafields.
I have a commerce 7.5 installation wich have become quite cluttered. How can I clean my installation from metadatafield to be able to import the data on a fresh installation? Under Administration / Catalog System / Meta Classes there is a button Delete. I have tried marking the metadata fields I want removed and pressing Delete. This just results in a message tha thet Item has been removed but no fields are actually removed. Any ideas?