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Yes, you are right. This is an important nuance, and trying to get around it by setting what can be scanned in this way and what can't will be quite difficult to implement. 
 
By the way, perhaps you will be interested in the experience of using the program, and how this request appeared:
I am engaged in nature photography, I take a lot of photos, after which I sort the photos into folders (categories of subjects) and further mark folders with successful photos for processing by adding them to favorites. 
 
A couple of times there was a system crash, with a heavy load on the graphics system, and was not able to complete the program correctly. As a result, all changes to favorite folders were lost, I had to repeat the selection again. I addressed the problem here, asking you to make the function of saving settings either automatically or manually, instead of restarting the program in order to save the program settings. You rejected the suggestion, arguing that it would put a lot of stress on the disk to save the settings. Probably restarting the program to save settings makes less load.  I am forced to use this method for lack of alternative methods.
 
This has led to a new problem. When sorting photos, I use the "Move to new subfolder" function, which has a convenient history function. But, as it turned out, no history is saved when the program is restarted.
 
After researching the program, I found an interesting ExternalEditors functionality that allows you to transfer selected files to another program. So I made an external file moving utility that has a history that is saved and a very handy filter. Thanks to the resulting combination of program and utility, sorting photos could have been a pleasure, if not for the... FRV does not automatically update the folder structure. And automatic updating of files as it turned out sometimes fails and does not work. So, as a result, this request appeared. 
 
In summary - I really don't understand the problem of saving settings automatically, either on command. Or making it more convenient to update the current folder by a single shortcut. All I see is an unwillingness to change anything. Sorry for that opinion, but that's the truth as I see it.

Sorry for the long text, I hope you are interested in the usage scenarios of your program and are interested in simplifying users' tasks according to the way they use your product.