If by "programs" you mean TV recordings or other media files, they were in your previous VU+ HDD.
So you can transfer by FTP clients like FileZilla or similar to an external USB HDD.
Or, more comfortably, you may use EMC (Enhanced Media Center) which is a plugin not only able to manage your media files but also to copy or move them to any devices connected to a VU+.
EMC can browse your devices.
By FTP you can do the same but you'll have to copy the all 4 or 5 files created by recordings and it's less comfy.
So by EMC you'll be able to copy from the USB disk to the new VU+ HDD.
If instead, by programs you meant plugins, my advice is to install them again because they can surely be copied this rough way, but a proper reinstall will set your system configuration files accordingly.