I think you misunderstood. Oracle supply a utility called "opatch". That is the utility you are using to do the lsinventory. The version that ships with the database is rarely the latest version. The first thing you need to do is download the latest version of "opatch" from M.O.S. and use that to check your inventory.
If that works, great. If it doesn't, then you need to raise an SR with Oracle Support (M.O.S.) to see how you can repair your inventory.
Typically, your inventory will be amended when you do your software installation, prior to the upgrade. If your installation of the new software has been successful, your inventory should be fine from them on. Upgrading a database will not have a detrimental affect on it. I don;t understand how you've got into this position, but assuming you can't remove and reinstall everything to sort out your inventory, your best bet is to progress this through Oracle Support.