It's not easy to guess based on how your data is distributed across your folders within Site Explorer. If you knew about half of your data was in a couple of subfolders you could try exporting lower levels of the tree, but then you'd skip higher levels. Not an ideal solution. The basic problem is that the packaged data must zip to 2GB or less.
Alternatlively you can copy the whole repository subdirectory to your new instance and either replace the installed set or place it in a new location and change the path references in the serverconfig.ini. For example the installed folders are defaulted to the c drive. If you created a set of folders on your d or e drive of your new machine that included the full "C:\Program Files\Autodesk\..." down to the server directory you could just edit the new serverconfig.ini and change the path from C to D or E without changing any subdirectories. You could also do this on a new install from Site Admin. Log out, restart your server. There are only a few path entries that include Repositories in them to change.
Dave