You cannot delete the QVD (or other) file directly from QS script. But you can use the "Execute" command instead (directly or with BAT file)...
But please note that you have to switch to "Legacy" mode to do so...
For the second question:
You need to specify all fields in the data table explicitly (using "Inline" structure) and store it into QVD to create an "empty" QVD file.
load * inline [
A1, A2, A3, A4, A5
store QVD_Table into [lib://Extractions (abc)/Test_empty_qvd.qvd;