You may or may not be having the same problem that I had. When I used the converter, it automatically created the mod folders in my A2:CO folder. As I wanted them in A3, I moved them into that folder - and then tried to patch them. After some trial and error, I realised the patcher seems to look for the folders in the A2:CO folder and - as I had moved them - the patcher was throwing loads of errors at me as it couldn't find the files to patch.