Manually reconciling an entry won’t remove it from the Account History. It's possible that the Check column was sorted out making the reconciled transactions appear at the bottom part of the register.
Let’s run a quick report to see if they are still available. Here’s how:
You should find all of your transactions depending on the set date range. Check out these articles for more information:
Everything you need to know about reconciliation can be found in this link: Reconcile hub.
That should get you back in line.
Let me know who this goes. I’m always here to help if you need further assistance. Have a good one!