Amending 2008 SA returns
HMRC are unable to process amended 2008 returns today (31 January 2010). The system will reject the return with a message "The window allowed for amending this return has passed" - or similar wording.
HMRC has asked that anyone trying to file an amendment to a 2008 return today should attempt to file and then take a print of the rejection message. They should then include this print with the paper return to show that they had tried to amend within the window. The amendment will then be processed as if it were made on time.
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CT Online had a similar problem
We had the same problem with amending a 31/12/07 CT return on 31/12/09: online filing rejected the amendment, saying it was out of time. In a strange way, it's comforting to know that it wasn't just us. We submitted on paper with the error message.