We are sorry to hear about the problem you have encountered.
The reconciled balances in Moneydance are calculated from:
Initial Balance of the Account + Cleared Deposits - Cleared Payments
To adjust the reconciled balance, you'll need to adjust one of these variables. Since your reconciled balance changed, that must mean that one of the following happened:
1) Your account's starting balance changed
2) One or more cleared transactions were either deleted, had their amount modified, or added
3) One or more transactions were marked (or unmarked) as cleared
Any one of the above would affect the reconciled/cleared balance of an account and could have caused the difference. Moneydance does display an extra confirmation/warning window when you try to do either 1 or 2 in the account's register.
Also,if you had the Mark transactions as cleared when confirmed enabled, in the Network section of the Preferences window, and you performed a download and confirmed transactions with that setting enabled, then those confirmed transactions would have been marked as cleared, affecting the reconciled balance.
So, to correct the problem properly, you'd need to reverse the root cause of the change in reconciled balance.
You could also get the reconciled balance back to the correct value by simply entering an adjustment, either to the account's starting balance or by entering an adjustment transaction and marking it as cleared.
Hopefully this information is useful. Do not hesitate to contact us again, if you need further assistance.