econnolly - you were the first one to clearly articulate the problem and point out that the Quickbooks helpdesk is not answering the question at all. I don't if they made a change to the software as I am looking at this issue six months later, but this is what I did and it appears to have worked.
My issue is that I have a Euros bank account with a zero balance in the underlying register (which is tracked in EUR), but the balance sheet (which is in GBP) was still showing a balance. I assume that the residual balance showing up on the BS is the result of exchange rate gains/losses that have accumulated in that account. As you pointed out, if you post an entry to clear out the amount on the balance sheet, that entry will also go down into the underlying register and affect the balance there (which is already at zero).
What I did was post a journal entry, but I selected GBP as the currency instead of EUR. Then I clicked the button that says "Home Currency Adjustment". On my version of Quickbooks desktop, this appears just to the right of the box where you selected the currency to use for the journal entry. I posted the AJE for the GBP amount that was appearing on the Balance Sheet with an offset to a P&L account "Exchange rate gains/losses". This has cleared out the Balance Sheet for the Euros account. And when I look at the underlying register, it is still zero. This AJE carried over to the register, but it carried over as a memo transaction only with a -0- balance.
