SCCM 2012 r2 Content Library migration to new drive and now software centre showing empty

Hi Guys,  I recently went onsite to a new client that has just gotten rid of its previous IT support company. They had a production SQL server and the previous IT company decided to install SCCM onto it which unfortunatly filled up the HDD to the point it almost ran out of space.

We installed some new drives into the Server, created a new partition and then ran the sccm tool - ContentLibraryTransfer.exe to move the sccm shares and data to the new partition.

this all worked fine no errors or anything. Able to see all the data within the SCCM Management console.  What i found out later in the after noon is that they also have System Centre installed on another server and now they have told me that ever since transfering the content library in the morning the system centre is not showing any applications, updates or anti virus definitions.

Is there any link between moving the content library and the fact that it disappeared from the software centre?
Is there any way i can get the software centre to re-populate all the information if it is linked to moving the content Library?


Any help would be greatly appreciated.  I am a complete beginner in SCCM and only reason i had to take drastic action this morning is because the main SQL server was about to go kaput.