Basically, the error is saying that the operation cannot be completed because the system cannot find the file CleanAppl.bin.

This is what I thought. I've instructed the customer to do this operation following carefully the instruction provided with the clean boot files. Thanks.

Sounds like it try to clean apps on wrong location, This can be happened if you are using new clean_app.hex - file, on older Flash. Can you tell me, What is the device's BSP? What it's memory size? (P/N)