No not exactly, I suppose that the service tax collected, even though under mistake of classification of service, has been deposited with the department. It's an offence if assessee charges a higher tax and does not deposit it with the department. Upto now whatever has been collected as service tax should go to government account.
In respect of modification in the ST - 2, I would say that it's an easy process. The assessee would be having his login at www.aceg.gov.in. ST-2 can easily be modified online and submitted online. You will receive the modified ST-2 after the cancellation of the previous ST-2 within a short period of time.
You may be aware of the procedure but for reference only follow the procedure:
www.aces.gov.in > Service Tax > Login > REG > Amend Registration > Select ST - 2 to be amended > make necessary details and after confirming the same submit the same.