Does the controller show any files after you deleted all the files? If not, then there are no files remaining.
Sounds about right, because the 128 MB flash memory also contains the controller’s firmware & settings.
Unless you’re in production where you (or the operators) frequently run the same jobs, use LightBurn’s Start option, rather than Send, to avoid filling the memory with files you’ll forget when the controller starts misbehaving due to overstuffed memory.
CAUTION: Do not, under any circumstances, run the Reset to factory parameters (or similar wording) operation, because it will blow away all the configuration applied to the machine before you got it. This apparently includes a number of settings that cannot be accessed by either LightBurn or RDworks, leaving no way out of the abyss.