User created an invoice without line items, but it did not affect the income account set at the project level.
This is the expected behavior in Core. The income account you set at the project level is carried forward to its time and expenses. So it is affected only when your invoices have time and expenses (as line items). Check the Core Help for details on this field. If no account is set at the project level, the one set in Global Settings is carried forward to the time and expenses, by default.
There is another setting in Global Settings > Accounting to specify the income account for invoices that do not have line items. Under Default Accounts > System Accounts, you can specify this account in the Income Account for Services/Expenses Without Line Item field. Check the Core Help for more details.