Welcome back to the QuickBooks Community, hkg48035. I'll ensure you can manage your loan and their interest in QuickBooks Desktop. Then, reconcile your account smoothly.
To start with, I suggest undoing the two years of entries to back out the transactions that are already reconciled in QuickBooks. To do this, you'll need to go to the Begin Reconciliation window so you're able to start the process. Beforehand, you'll need to Back up the QuickBooks company file.
- Go to the Banking menu at the top and select Reconcile.
- From the Begin Reconciliation window, select Undo Last Reconciliation.
- When prompted, select Continue and click OK.
- Close and reopen the Begin Reconciliation window.
Once done, you can now use the QuickBooks Loan Manager to help you calculate interest and payment schedules. Then, please make sure to monthly reconcile your bank entries to avoid discrepancies.
On the other hand, yes, the individual entries can be marked as reconciled without disrupting the checking account. You'll have to go to the Chart of accounts and choose a specific account, then you can manually checkmark entries. This is to confirm that transactions are already reconciled. Please follow the steps below:
- Click the Accountant menu at the top. Then, choose Chart of Accounts.
- Select a particular account.
- Choose a specific entry and put a checkmark on the Checkmark column.

Lastly, I suggest consulting an accountant to provide suggestions on how to properly handle your loan and calculate interest correctly using a liability account and the interest account set up on the program. This is to ensure your records are in shipshape.
Lastly, you may refer to this article to view various guidelines that might help you in fixing any reconciliation issues in QBDT: Learn the reconcile workflow in QuickBooks.
If there's anything else I can help you with, aside from managing your loan or other transactions, please let me know by leaving a comment below, hkg48035. I'm always here to help. Have a great day!