As is... what ConEmuHk is doing described in ConEmu docs.
In brief - it fixes many Win console problems and implements "inprocess" features like ANSI and "-new_console".
Internally - it hooks dozens of WinApi functions.
In theory, it must not break any behavior of running applications, but if it so - you need to report the problem on project issue tracker.
PS. Do you using last ConEmu build?