I have just found the solution to the problem (2 minutes later XD)
Quote CodeJunkies' Support site:
Try resetting the Action Replay by following these steps:
- Insert the Action Replay into the DS
- While the Action Replay software is loading, press and hold all the following buttons: A + B + Start + Select.
- Release all of the buttons once the Action Replay is at the main menu.
The first screen should persist for much longer than normal, and when the Action Replay DS main menu loads, your hardware should be reset.
Once the reset has been performed, try connecting the USB cable to your PC, opening up the code manager software and transferring data again.
It won't return all of your games back, but it will allow you to start on a clean slate again. (Using the update feature will bring most, if not all of your games back
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