You are hitting a hard limitation with how Jobber’s QuickBooks Online integration is built.
Jobber’s sync engine maps Client to QBO Customer. It does not sync to QBO Projects, nor does it turn individual Jobs into QBO Sub-Customers.
Jobber will sync multiple Properties under a client as QBO Sub-Customers (Client Name : Property Address), but it cannot isolate individual job numbers or work orders as their own QBO Sub-Customers or Projects. Any invoice synced over lands on the main Client or Property profile in QBO, which forces you to manually move those transactions if you rely on QBO Projects for tracking.
Jobber built the sync this way because they expect you to track job costing and profitability inside Jobber's internal reports, while using QBO strictly as a general ledger for overall income, expenses, and taxes.
If your accounting workflow requires tracking individual jobs inside QBO Projects, you really only have three choices right now. First, you can continue manually reassigning invoices and payments to Projects inside QBO after they sync over. Second, you can shift your job costing and project reporting over to Jobber’s built-in reports, letting QBO just hold the high-level financial data. Third, you can go to Settings, then Give Feedback in Jobber and submit a feature request for QBO Project Mapping.
Bottom line: Jobber handles Properties as Sub-Customers, but it will not map individual Jobs to QBO Projects. Until Jobber updates their sync architecture, there is no automatic native way around the manual work inside QBO.