Oh, wow! Eddy! You may have produced the most useful plugin in a long time! (I don't mean YOU particulary, I mean "all of us").
I wait for it with 'bated breath!
LLoyd
I can't believe that for one minute.

Try the attached. Please note version 1 may fail in some instances until testing is complete.
Also no UNDO added yet.
1. make a new drawing with 2 polylines, closed or open, they do not need to have the same number of points.
2. assign some MOPs to ONE of them and generate toolpaths
3. run the plugin, Plugins->Polyline Replace
4. select the first line, the one you assigned MOPs to, hit Enter
5. select the second line, hit Enter
6. Now just generate toolpaths again and all should work.
Having to go out for a while so I just wanted to get this posted first.
Edit: See my first post for the latest verison.