@quid, I finally took a look at the tag 'topology'. I apologize for taking so long. The tag 'topology' is a mess, so I am not completely sure. Nevertheless, I would think that the best line of attack is the one you suggested. Retag all (or most of) the questions which do not have a top level tag, and perhaps also (some of) the ones whose existing top level tag does not relate to topology. Then merge the tag 'topology' with 'tag-removed'.
By the way, @quid and others. Do you happen to know what are the precise criteria under which single-use tags are deleted? I could not easily find a reference. Thanks.