Although the link is from a very old post the following quote is still relevant:
So if you are changing systems part way through the year take the year to date (YTD) P&L report and do a journal entry with a line for each individual income and expense account, with the balancing line (net profit/loss) to Retained earnings account. The balancing line in the journal to Retained earnings will be a debit for a profit or a credit for a loss. This seems counter intuitive, but the Retained earnings line represents a reversal, as this amount is contained in your balance sheet starting balances and the system will generate it again as a result of this journal.