I'm using srrGUI on a laptop and slipped on the touchpad, resulting in me accidentally dragging a folder into another one while selecting the Input Dir Path. This folder I accidentally dragged is now no where to be seen! I did a full search of the entire laptop using Agent Ransack including hidden files/folders and failed to turn up this folder I had dragged into another one!
My conclusion is that srrGUI has bug when selecting using the Input Dir Path popup box, if you drag a folder into another one, it fails to move the folder properly and the NTFS is not updated, resulting in the folder vanishing.