I would recommend you use the QMC to control your reloads. It gives you the option to trigger one reload after another completes, provides access to reload history and timings and can send emails if reloads fail.
Use the QlikView server to do what it is designed for rather than using batch files.
About the only reason I know why people use qv.exe to reload a server document instead of the reload engine is that without a full Publisher, reload schedules are less flexible that what is required. A Publisher can reload according to almost any schedule imaginable, but has a price. The reload tab in SBE without Publisher only does simple repetitive reloads, and only one per document.
Most people with complex reload requirements switch to qv.exe together with Windows Task Scheduler.