Wouldn't be easier to just use ADE to edit the airport ?
As an alternate solution, you could first decompile the AFCAD into XML format using ADE (just compile it, there's an option to keep the XML file), and keep that with a new filename.
Then, edit with AFCAD, open it again with ADE, decompile again into XML, open the XML you saved before, take the exclusion zones commands from it, open the XML derived with the AFCAD-edited version, paste the exclusions into that, and finally compile with BGLCOMP...
It's probably easier to use ADE...