If you do a partial refresh, all unchecked elements will be considered removed from the relational model data. Are you sure you want that?
Even with that, removed entities from rel. model data are not removed from your model, but the field mappings are removed (because there is no rel.model data information for that entities), but the TypeConverterToUse remains in the entity filelds.
So I can't reproduce it. BTW the latest build is June 17th, not May 13th.