To ensure the relational integrity of the Quick books set of files make sure you backup a quick books QBB file.
Use the Scheduled Backup feature in QuickBooks to create a backup prior to the Backup Schedule running.
Step 1:
1 - Open QuickBooks to the company file that you wish to backup.
2 - Go to the File menu.
3 - Select Save Copy or Backup.
4 - What type of File do you want to save? Select Backup copy, and click Next.
5 - Do you want to save your backup copy locally or online? Select Local Backup, and click Next.
6 - When do you want to save your backup copy? Select Only Schedule future backups, and click Next.
7 - When do you want to backup your company file? Click on the New button. This will open the Schedule Backup window.
8 - Enter a Description for the task (ie. Weekly Backup_Monday_[File Name]).
9 - Click the Browse button, to select the location to which QuickBooks will save the *.qbb file. You will want to select a location to which the  backup client can access the file.
10- If you wish to only keep a select number of set number of backup copies for this file within the designated location, place a checkmark in the box labeled Number of backup copies to keep. You can then enter the number of copies you wish to keep.
11- Under Select the time and day you want to save the backup:
Start time: Enter a time that you'd like Quickbooks to automatically backup your company to the specified folder above. Since the backup uses a continuous data protection process, any time will work.
Note: The Scheduled Backup process will only backup the QuickBooks Company file if the file is closed prior to the Start Time of the Scheduled Backup. If the file is being accessed in a multi-user environment, all users must be logged out of the Company file.
12- Click the Store Password button. This will open the Store Windows Password window.
13- Enter your Windows username and password. QuickBooks stores this information for you so that the backup can run at the scheduled time.
14- Click Ok, to save the information and close the window.
15- Click Ok, to save your Scheduled Backup settings and close the window.
16- Click Finish.
Then make sure the Quick Books Backup folder is selected by the backup client for backing up. 

See FAQ:

Folder Selection