if i understand you situation, you have a QVD generator and the QVD created was deleted and now your qvd generator doesnt create the new QDV when run.
the QVD generator (specifically the store command) doe snot require the QVD to be present. therefore something must be wrong with your code. the act of deleting the QVD file did not cause the issue it is somewhere else. maybe sharing your code would help others figure out the problem for you