I understand the urgency of this matter, @LINKConstruction. Let's get this issue resolve.
 

To recover the deleted invoice transaction, you can recreate the transaction and apply payment if necessary. 
 

Meanwhile, for your first concern, you can create one deposit for multiple invoices. From there, you can pay the individual customer.

Here's how to create Bank deposit:
 

1. Select + New.
2. Select Bank Deposit.
3. From the Account dropdown, choose the account you want to put the money into.
4. Click the checkbox for each transaction you want to combine.
5. Make sure the total of the selected transactions matches your deposit slip. Use your deposit slip as a reference.
6. Then Save and Close.
   
   

For additional information, you can refer to this article: Record and make bank deposits in QuickBooks Online.

In case you want to run reports in the future you can check out this article: Run reports in QuickBooks Online.
 

If you need anything else feel free to come back. I'll be happy to assist you. Stay safe!