Even if you don't clear it, when you scan the new location they should show up and the old location won't show up when not connected. This is how it seems to work with the two USB drives I use when taking one of my Boxes with me. If they aren't connected those items don't show up with my network content. And when I have the box at another location, only the content on the attached USB drive shows up in my Movies list.
If I have the USB drive connected and it's also connected to my network at home, then when I select a title from the coverart, it will show both locations and I just select whether to view the title from my network location or the USB drive location.
Boxee Box 1, 2 & 3(Boxee+ v1.4.6), PCs(v18.104.22.16896) Boxee TV(v22.214.171.12481)
Server 1: HP MSS WHS (56TB) (NFS/SMB)
Server 2: unRAID (32TB) (NFS/SMB)
Server 3: unRAID (27TB) (NFS/SMB)
Server 4: TiVo Desktop (6TB RAID 5) (SMB)
NAS 1: Intel SS4200-E (4TB RAID 5) (NFS/SMB)
NAS 2: Dlink DNS-321 (1TB RAID 1) (SMB)