Welcome to the QuickBooks Community @LPurciello.
I am happy to help you work on clearing up this up today!
Instead of deleting accounts that are connected to online banking, we recommend disconnecting them. This way, QuickBooks will not download any new transactions but keeps transactions that are already categorized. It will also remove any transactions that need to be reviewed.
When you delete an account, rather than disconnecting it, if there are transactions remaining in the account that were deleted, they will remain in the checking account.
For example, if you deleted your Paypal account, but previously made payments to Paypal from your checking account, the payments will stay in the checking account. This is probably why you are seeing this discrepancy.
Here is a great article that will help you add the transactions missing from your account: Manually upload transactions into QuickBooks Online.
If you have additional questions on this or anything else within QuickBooks Online, please know I am here to help! Take care.