I am thinking about the Bash job control with fg 1 and bg 1 and maybe pengine_rpc/2 or some other pengine related idea.
Theoretically I guess that should be possible. As is though, two threads reading from the console make a mess. Best options are swipl-win (both the Windows version and the Qt version) or use the libssh pack that allows to login into Prolog using ssh. For the latter, make sure you use the libedit based commandline editor to get commandline editing on each connection (libedit can have multiple editor instances where readline only has one).