If you create a track of within your route in Basecamp then transfer to the Nav 6 you may be able to see where the Nav6 has changed the route on transfer.
Not wanting to sound like teaching your granny to suck eggs, I am assuming you already know how to do this, but if you dont...
Create the track by right clicking the route in Basecamp and select "create track from selected route" in the lower LH window of Basecamp
Once transferred along with your route (basecamp transfers both route and track together) you want the track to be visible on the map, to do this go to:-
Apps > Tracks > select your track > spanner Top LHS > Click Show on map > Then set colour (I always use black).
This will put your carefully built Basecamp route on the map as a "drawn line" It doesen't change on transfer.
However, unfortunately the Nav 6 layers the magenta route over the track obscurring it, well mine does, (all older Zumos lets the track layer above the Magenta route so its clearly seen) so you may (if you have the patience to scroll through the map view on the GPS) notice somewhere along the route where you can see the black line appear from the magenta route taking different roads this is where the changes will be made on transfer.
I appreciate not the easiest way to figure it out but might show where its recalculated.