You'll have to notify Cryptsy of the source change, and even then they may not switch since it's not official code.
I opened a support ticket with Cryptsy almost two weeks ago. It's still "being processed".
They usually handle switchovers in less than a day. Might be delayed because it's not the official source, or maybe they just forgot lol.
You guys should try and track down whoever owns the official github and get them to merge.