but they send me file number ..why?
Usually when CIO send a file number, it means that a desision has been made, so in your situation, i think it was a refusal not sending back the entire package, because they did keep a records for your file and cashed your money order as well.
I am sure that they cashed your money order didn't they ? and they didn't send you the entire package back just a refusal letter with file number confirming the refund ?
this mean the reply for updates will be fast or 3 months ?
Whether they send back the entire package or just a refusal letter with file number, they take the same time as a new application, if you want to re send a new application, because it has to go through the queue again based on the date of reciept.