When reconciling, if the difference is not zero when you are finished, but the amount isn't off by very much, you have the option to make an adjusting entry. Taking hours to find amounts that are off by a few pennies doesn't make much sense.
Adjusting entries should be made only as a last resort for small amounts. Making adjusting entries for substantial amounts may create serious issues in the future. We recommend that you ask your accountant before making any adjustments.
How adjusting entries impact accounts
If the difference after reconciling is a negative number, create a check transaction, without a check number, which will reduce your bank account and your Opening Balance Equity account by that amount.
If the difference after reconciling is a positive number, you'll create a deposit transaction, increasing your bank account and your Opening Balance Equity account by that amount.
These adjustments affect only your Balance Sheet, not your Profit & Loss.