then I would go down to the Inspectional services department for the City of Boston which is located at 1010 Mass Ave. You are more likely to speak with someone if you show up in person. There are city codes and regulations, and then Charlestown may have some neighborhood requirements. 1010 Mass Ave will let you know if there is a Charlestown Historical Commission that also needs to weigh in on the process.
So your answer depends on why it was illegal in the first place!
Another thing is that your deck should not exceed snow load (decks are heavy). And consider that your rubber roof (I presume) may need a repair.
Here is much info about roof decks: http://www.coolflatroof.com/flat-roof-decks.php