I think you can do this with a single substitution regex (s/pattern/replacement/;), but it's going to need a lookahead assertion at the end. Also, this is only possible if you can write a regex segment that will consistently match the metadata. (Making it match metadata if there is any and not block matching if there isn't any is then trivial: precede the metadata-match portion in (?: and follow it up with )*.
Perhaps something along these lines...
s/(a(?:[<][^>]+[>])*)a((?:[<][^>]+[>])*(?:\s+|[;,.])+)/$1$2/;
That appears to work with the actual sample data you provided, but I don't know if it will work with your real data.
