M588 S"*" will clear all the networks. You can then re-add with M587.
If you are getting responses from the firmware there is nothing corrupt.
Can you send M122 and copy paste the results here?
Make sure your line endings in YAT are set correctly.
yat.png
Can you show a screen shot of what your SD card folder structure looks like now? What version of firmware and DWC files did you use?