If I understand your question, no you would not have to re-import all of your previous scanned faxes, etc. That would be a nightmare. All of your imported items are in a folder called ImportItems in your Amazing Charts folder on your server or main computer. It is this folder that HAS to be backed up nightly. But, if say, your SQL database became corrupted, you would restore from your AmazingCharts.enc file. The folder would still be intact and you would be all set. You can move the folder anytime you wish.
To get a feel for it, open the folder and you will see subfolders for any patient you had to import to. Then import something into a different patient, and a folder will be made automatically.
This is a perfect example of what David is talking about when he says the AC automatic backup is but one piece of the backup.