How to use batches in File system scan

Hi!

I am curious about using the new batch feature since we have a lot of folders (from 1980 to 2024) but I wonder if I am selecting or de-selecting folders when I click them?
I.e., should the icons of the folders I want to include in the batch be blue och black? ??

Also, I removed a folder from /uploads that was from an old plugin we don’t have anymore but the folder + subfolders still show up in the batch list, how can I get rid of them? The folder had a lot of subfolders, so depending on the answer to my first question it can be a lot of folders to click when making a batch.
I have only tried it locally so far, using XAMPP, no change when I restarted everything.

Thanks in advance!