I appreciate you for joining the thread, @BeerOutside. I'll share an insight about how the reconciliation works inside QuickBooks Online (QBO).

Please know that once you've reconciled a transaction inside your company, it'll automatically be added to the appropriate account in your Chart of accounts. That said, a reconciled transaction won't be missing, but rather gets added to the prescribe account. 

What you'll want to do is to exclude only those duplicate transactions to avoid getting them mixed up with all your existing bank transactions inside your account. Once done, you can proceed with the merging of accounts in your COA. I'll input the process below to get you going. These are the steps:

1. If you're merging accounts that have reconciliation reports, save those reports first. The account being merged may not keep the reconciliation history. The transactions remain on the merged account and stay reconciled. A reminder, if both account registers have an opening balance equity transaction, you'll need to delete the transaction with the most recent date prior to merging. The older transaction becomes the opening balance of the newly merged account.
2. Go to the Gear icon, and then select the Chart of Accounts.
3. Find the account you want to keep. Then, select the dropdown ▼ in the Action column and then Edit.
4. Note the Save account under (Account Type), Account name (Name), and Tax form section (Detail Type) of the account. These must be the same between the accounts you want to merge.
5. Check if the account is a subaccount or parent account. The names of subaccounts are indented in the Name column of the Chart of accounts list. If it is, note the parent account it's tied to.

For further guidelines, please see this handy article: Merge duplicate accounts, customers, and vendors in QuickBooks Online.

Additionally, I've got you this article to help you troubleshoot accounts you've reconciled in the past: Fix issues for accounts you've reconciled in the past in QuickBooks Online.

Also, I've got you this article about modifying reports and adding extra details to it so you can monitor all aspects of your business: Customize reports in QuickBooks Online.

Please don't hesitate to post here again if you need further assistance with this, @BeerOutside. I'm more than willing to help you get out of this situation. Stay safe, and have a nice day!