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 CORE Help Center for details on this field. If no account is set at the project level, the one set at the global level in Settings is carried forward to the time and expenses, by default.
There is another setting in Settings > Add-ons > Accounting to specify the income accounts for invoices that do not have line items. Under System Accounts, you can specify these accounts in the Non-Itemized Service / Expense Income fields. Check CORE Help Center for details.