When you say "How to remove transactions from feedback box that remain because seller left no feedback" do you mean "How can I revoke the feedback that I left for the seller if the seller fails to leave me any feedback?" If that is indeed the case then the answer to that question is that it's not possiible. Once you've left feedback for a buyer or a seller it is not possible to revoke it, although if eBay saw something in the feedback that they felt breached their rules as to what you can and cannot say in your feedback comments (eg: abusive/racist/sexist comments) then eBay can remove the feedback themselves.
With regards to leaving feedback for a transaction where the listing was subsequently removed by eBay after you had made the purchase it is not possible to leave any feedback in relation to that transaction.
