Hello.
I just ran into the very same problems described in here, and none of the solutions helped my situation... but they did point me towards the correct direction. I'm posting my solution here in case anybody else with my same condition arrives here as well - just as I did.
In my case, I had created a controller in slot 1, faulted, and it did not allow to be removed... but when I checked in RSwho, it detected it as RSLinx Enterprise, desktop.
So, all I needed was to open the windows Process Manager (Ctrl+alt+del, processes tab) and stop RSLinxNG.exe.
Restart RSLogix Emulate 5000, and this time it booted the controller without any trouble! so I now was able to delete it... an create another one in the second slot.
I rebooted my machine, opened the emulator, and there it was, RSLinx Enterprise was for some reason fighting the emulator for slot 1, so when I instead switched to use slot 2 it all worked out. I jsut had to stop the enterprise version first for the emulator th be able to let go of the slot.
Hope this helps somebody in the future... I've lurked here for years, first time I've found a reason to create an account was to actually share this with whoever comes looking for it.