We use a shared config setup so I turned that off and then made the zip file using Web Deploy (V3). When I moved it to the new machine it had only grabbed one site. We have a bunch (about 1600+ sites). Is there some option I'm missing to get it to grab all of the sites?
FYI, when I first ran it gave me: AppPoolNotFound dependency check found the AppPool 'x' to be in use by the source data but not defined in source data or on the detination computer...
I then ran it with ' -enableLink:AppPoolExtension' and that appeared to work. Well, it didn't give AppPoolNotFound error but as I stated, it only did one site.