You are looking at the node technical systems ->ABAP -> software, so you are checking a product instance.
A product instance comprises a defined set of software components. This list is what you see in the screenshot.
Your 7.31 software components are not gone missing. They just will not show in the place you are trying to check them. You have to go to the software component versions tab to see all.
You have to add product instance EHP6 for SAP ERP 6.0 - Central Applications. You have right now just the SAP ERP 6.0 part of the definition. Don't remove SAP ERP 6.0! You need to add EHP6 for SAP ERP 6.0 also , though.
No need to add EHP3 for SAP Netweaver 7.0 .
Best regards,
Miguel Ariño