I understand the importance of keeping our records organized, @Matthewmckerrow. I'm here to help you out. 

In QuickBooks Desktop (QBDT), we can review the imported IIF Files by accessing the account associated with the file. If there is indeed a duplicate, we can batch-delete it. 

Beforehand, please take note of the following: 
 

• The Batch Delete/Void utility is only available in QuickBooks Desktop Accountant 2018, Enterprise and Enterprise Accountant 18.0, and later versions. 
• Sign in as an Admin or External Accountant user.
• The Batch Delete/Void Transactions tool doesn't support multi-currency. 

To Batch Delete/Void, follow the steps below: 

1. Go to the File menu and select Switch to Single-user mode. If you see Switch to Multi-user mode, don't select it.
2. Go to the Accountant menu and select Batch Delete/Void Transactions.
3. Choose the transactions you want to delete or void from the Available Transactions list.
4. Click Review & Delete (or Review & Void).
5. Select Back Up & Delete or Back Up & Void. You can also skip the backup and select Delete only or Void only from the dropdown menus. 
6. Hit Yes to confirm. 

However, if you're using the unsupported versions, we have to manually delete the transactions individually.   

Alternatively, if you have a backup company file, we can use that instead and import IIF files there. Using your backup company file eliminates the need to manually delete duplicates and ensures a clean slate for work. 

Moreover, I'll add this article about managing the IIF File in QBDT: Export, import, and edit IIF files. 

You're welcome to post here in the Community space if you have more questions about IIF Files. Keep safe!