There are a few resources on the help site regarding automating publishing services:Publishing from a map documentPublishing from a text fileWhen you publish to ArcGIS Server, an MXD and MSD are placed in the arcgisinput folder within the site, Ex. C:\arcgisserver\directories\arcgissystem\arcgisinput. What you can do is loop through this directory for the mxd's and then publish them to your other ArcGIS Server site. The thing to make sure of here, though is that all data workspaces in the old server site are registered with the new server site. Attached is a script tool and script I wrote a bit ago to write the workspaces of mxd's in a directory to a file. This can be used to check the workspaces of all the mxd's you have published and register them.What you can also do is loop through the directory as described above, and follow the documentation below to register data sources at publish time:Register a data folder at publish timeThe main thing is to make sure your data sources are registered correctly in your new server if you're going to automate this process.