If you run a Backup, it backs up all the files under your practice data folder, including subfolders.
If you run a Backup Root Data, it backs up all the files within your Medisoft Root Data folder (usually C:\Medidata), but it does not include any subfolders. You only need to run this after registering your software or after you add a new practice to your practice list. I have found the Restore Root Data function to be unreliable, but if you work with a value added reseller, they should be able to restore your root data folder manually from the backup. Alternatively, if you keep a printout of your registration information, that should be all that you need from your root data. If you need to restore to a new computer, just key the registration information in and your are good to go.
We offer a backup service called HIPAA Backup Service
if you need it.