The protection of folders performed by Folder Guard may confuse some of the system utilities, such as the backup or disk managing software. For example, if your backup software allows you to specify which folders to include in the backup, and you leave the protection in effect during the backup, the folders you've made hidden with Folder Guard may not be backed up. (On the other hand, if the backup software stores a complete image of the disk disregarding its folder structure, it may be safe to leave the protection on, since Folder Guard does not prevent the direct access to the disk sectors.)
To avoid such problems, you could add your backup and disk utilities to the Trusted list of Folder Guard:
Originally, the Trusted list contains several system programs that must have full access to all files and folders on your computer in order for Windows to operate properly.
When performing the protection, Folder Guard intercepts the requests from programs to open files, list the contents of folders, etc. If such a request comes from a program that is designated by you as a trusted one, Folder Guard passes the request on to the operating system without any intervention, thus allowing the program to have a full access to all folders on your computer. If the path of the program is not in the Trusted list, Folder Guard allows or denies such request according to the attributes of the files and folders set up by you.
In other words, the Trusted list overrides other restrictions you might have set up with Folder Guard. For example, you could create a filter with Folder Guard that would deny access to a specific folder for a specific program, but if you add that program to the Trusted list, the folder will be fully accessible for that program. If you want to fine-tune the restrictions for a specific program, remove it from the Trusted list first.
Note that only Windows applications (64-, 32-, or 16-bit ones) can be designated as the trusted ones. You may add a DOS program or a console application to the Trusted list, but it will not have any effect.
You may wish to add to the Trusted list the system tools such as an anti-virus utility, a disk defragmenter, a disk scanner, a backup utility, etc. If you do so, you won't have to manually disable the protection before running such tools, since they will have a full access to all your folders and files anyway, as if Folder Guard was not present in your system at all.
You probably don't want to make programs such as Explorer trusted, because if you do, they will be allowed a full access to all files and folders, even to those you have hidden or password-protected!
Some programs come with several program files located in different folders. For example, Windows Notepad usually has 2 such files (notepad.exe), one located in the C:\Windows folder, and another one in the C:\Windows\System32 folder. In situations like this you should add both such files to the Trusted list. (You may want to use Windows Search to locate all program files on your computer. Or use Windows Task Manager to see the file locations of the running tasks.)