GST/HST remittance report to be fixed after year end

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Hey everyone, 

I'll try to explain this the best I can to see if you can help me. I was 3 months into entering when I learned that the HST sales tax was set up incorrectly. It was fixed but of course as we know previous amounts wont show up on the report when doing remittance. I should have deleted the re-entered the receipts but I didn't. I didn't realize at the time that would be the best solution. Now the year end has been complete and my accountant sent everything in and told me it has to stay the same and not change as its already sent it. Which I get so now the report each time I do my remittance for GST the number is off as it is missing the first bit of transactions. Suggestions on how to fix this without going back into last year??