I contacted with the Autodesk Team Support and they gave me the solution. This is the Autodesk answer:
"For this issue, please load the Inventor add-in "EDM Add-in." It is hidden, so you will need to choose "show hidden" inside of the Inventor Add-in menu".
Thank you for your help!
Also, just to keep a record on this thread. I had Open/Place option greyed out and was missing Vault option above the tree menu. What fixed that was reloading Project file. Clicked on random project file once all files are closed and go back to the original. I think this glitch has to do with iLogic.