Here is a help topic that might be useful:

https://proconnect.intuit.com/support/en-us/help-article/back-data/copy-back-client-files-using-pros...

As they warn you, and in general when using any program that has its own built-in Backup function, it's best to set Carbonite, Mozy, Dropbox and similar tools and services not to backup your working files and folders (real-time sync), but point that service to the backup folder and let the program you are using control making the backups. That's because syncing in-use files isn't a backup process; it's a mirror process. These types of files that really are database-type structures don't do well when mirrored while in use.

I realize this is of no help if things are lost, but it also helps prevent the discovery that something is there, but corrupt and still not able to be used.

And you can use both functions, if it makes your other functions easier to manage. Have your routinely-updated mirror process, and also every evening make a true backup of newly updated files from the function internal to the program(s).