If the product with variation is listed, eBay refuses to delete the related variations. As a consequence, also eDock is forced to avoid this possibility to its clients. The only way to cope with this operation is to update the variation you need to remove with quantity available equal to zero. An alternative could be the cancellation of the entire product father and the creation of a new one without that variation.
Important: It is not possible to update the values of the variations that are already listed. if you update the values of that variations, the listing related to that variations cannot be updated!