I've been through this situation many times and I know its more difficult when agent is showing the "not reporting status" in console. You can't even run the reboot task in such cases from the Enforce Console - Agent overview.
SC STOP EDPA dosen't help, I know have tried that myself.
What I would do normally in such cases is that use the service shutdown tool (service_shutdown.exe) which comes with the DLP installation binaries from fileconnect. Simply copy this tool to "C:\Program Files\Manufacturer\Endpoint Agent" and run it through command line. It would prompt you for the tools password and your services would be stopped.
You then net start edpa and net start wdp later. This completes the stopping and restarting of services.
When the number is more, I would even store this tool on the shared drive and run these commands using psexec. Let me know if you need to know the syntax & I can share the same with you. This normally helps me restart DLP services on a large number of broken DLP agent without having to restart them.
example: psexec.exe @hostlist \\share\service_shutdown.exe -p___