If you can figure out all the APs that need to be moved into a folder, and there's a criteria that makes it easier to view them, then you can use 'bulk edit'.
1. Sort by whichever criteria puts the APs that go into a folder closest together (name, mac, IP, VisualRF floor plan aka 'Location')
2. Select the 'modify devices' wrench above the list table
3. Select the devices that you want to move
4. Below the table -> select group / folder and then 'move'
Img1: Modify Devices leads to checkboxes next to Devices
Img2: After selecting devices to move, move options are found below the list table
You can move devices between group and/or folder this way.