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I appreciate you joining in this thread, aqadir.
I'm here to share some information regarding linking existing invoice to a project in QuickBooks Online.
This message will pop-up if you're linking an invoice that is already linked to a transaction like, estimates and billable expenses in QuickBooks Online. 
Once you hit OK, the invoice value will be zeroed out since you're removing the linked transaction that has the original amount. To avoid getting this message, I'd suggest to check the invoices before linking them to a project.
There are two ways to know if an invoice is linked to a transaction, see the sample screenshot below to see where to check those linked transactions.
I'd suggest going through the resources below. These links contain more information about other ways to deal with the project feature as well as designing and customizing your invoice template:
Customize invoices, estimates, and sales receipts in QuickBooks Online
Let me know if you have additional questions. I'll be available in the comments to assist you further. Have a nice day!