Just look at the SAP Notes. I was facing a similar problem but that was with the deliveries ..the PGI was done and still the status was being shown as in progress instead of being complete.
I used t-Code : VL_COMPLETE (SAP Provided it in some notes).
Or either way you can check the logic of VFx3; to find where is it picking the invoices from (table name) and then manually edit the status in that table (you can use &SAP_EDIT for Standard Table)
or in case there are enhancement points available in VFX3, then you can ask your abaper to manually add a condition to ignore a list of invoices (you can either get these invoice numbers hardcoded or can get a table (with maintenance generator) to have the values of the invoices to be ignored from VFx3.