The problem doesn't depend on pywinauto or any other GUI automation framework, as far as I know.
The widely known workaround for the problem is Remote Desktop (RDP) session which provides necessary GUI context needed for GUI automation. If you have an ability to connect to remote target machine which should run your automation task, just keep RDP session running and do not minimize RDP to the taskbar. Machine with running RDP can be locked by Ctrl+Alt+Del safely for your automation tasks on remote target machine that is also locked.
Hopefully, it should help.