Hm, that's tricky (it would be easier with audio tracks). You won't lose your placements, but there will take some effort to achieve your goal. ... mind you - that's a shortcoming of Nuendo, not MIR: Due to the fact that Steinberg's DAWs aren't able to change a track from one channel configuration to another by means of a plug-in (e.g. stereo to surround), you will have to route each instrument to dedicated 5.0 group manually.
A step-by-step guide:
0. Turn down the monitor volume - some burst and crackles might happen.
1. Create a 5.0 Group Channel for each Instrument Track (... name them accordingly to make things easier).
2. Route each Instrument Track to the respective Group.
3. Drag the MIR plug-in from the Instrument Track to an insert slot of the respective 5.0 Group Channel. The plug-in will show an error message saying that there's a channel configuration mismatch - that's ok! ;-)
4. Make sure that there aren't any stereo instances left, save your project under a new name and close it.
5. Make sure that MIR's Main GUI has closed, too, or do it manually from the task-bar (right-click > Quit).
6. Re-open the saved project. All instances should now be alive again, in 5.0 configuration.
7. Select a 5.0 Main Microphone setup in MIR's Output Channel.
... that should do the trick.
There are other workarounds which make use of the "Force Number Of Output Channels"-option in MIR's Preferences, but this might not be necessary in your case.
HTH,