Hi Dave,
If your upsampling doubles the latency of that tool, your music will be affected by it (in my opinion)...even if you have it set to offline render.
There is a 'latency compensation' in Sonar that uses the latency that the tool reports to Sonar and alligns all your tracks/busses so everything stays in sync / correct on the timeline.
In my opinion / my ears, this is not undoing/deleting the latency unfortunately, but it's just alligning it.
There are other opinions/ears out there...
Personally if I had a synth part that needed upsampling, and it's something like a stringpad, or simular...I would freeze that track.
That iic will bypass the Sonar latency compensation, and leave the latency just in that stringpad.
Again, this is just what I'd do, I don't claim any truth etc.
I thought the upsampling is another great thng we learned from Anderton sharing this with us.
Learned a lot from him and always like his posts/vids etc.