There are a few ways I can think of how to do what you want.
Option 1: Mount one of the directories in DOSBox. When you need to switch to another folder, rename the original folder to something else and rename the folder you want to switch to as the original folder. Press Ctrl+F4 in DOSBox to reset diskcaching.
Option 2: Make floppy disk images of the original floppies and mount them in DOSBox. DOSBox doesn't support mounting multiple floppy images so you'd have to use another program like Virtual Floppy Drive to mount/switch the images.
Option 3: Make iso images of the folders. For example, Folder2Iso can do that on Windows. Then mount the images in DOSBox with imgmount and press Ctrl+F4 to switch between images. You can't save any changes to the images in DOSBox.
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