£100 SA late filing penalty received for 2010/11

Hi

One of our clients has submitted a paper return for 2010/11 himself. It seems the return was submitted on 1 Nov 2011 therefore the penalty. If we file an online return for the same (as an amendment) before 31 Jan 2012, will it be accepted as a return submitted in time? Is there any possiblity of cancelling the penalty? There are no tax liabilties as such.

Thanks.