Let's get your reconciliation difference down to 0 so you can proceed.
Since you mentioned that the exact amount you entered on a journal entry is also the same amount showing as the difference, let's focus on the journal entry in question.
If it doesn't appear on the list of transactions on your reconciliation page, it could have been deleted. To check, You can open the Audit Log page.
Click the Gear icon.
Select Audit Log.
Search the list, and see if the journal entry in question is there.
If it's indeed deleted, you'll have to recreate it. At this time, there isn't an option to undo a deleted transaction.
If the transaction in question isn't deleted, then I suggest reviewing the date you entered. If the date on it isn't included in your reconciliation date range, it won't show up on the reconciliation page.