Sharke are you going about this the correct way. This the way I would do it:
Create your initial session at 44.1K get your VST synths playing at 44.1K as well. Get the music all correct. (At this point you may want to render these parts out at 44.1K audio as a backup) Leave all the other 44.1K audio alone. It is only synth parts you are interested in.
Save all those synth parts you want to up sample as
Midi tracks. ie Midi data only. Have a 96K synth rendering session now:
Create a new session at 96K right from the get go. Insert the same VST's and load them up with the same presets. Set the tempo of the session the same as it was at 44.1K.
Now import those
midi tracks you generated at 44.1K and get those midi tracks to play your VST's now except this is all happening at 96K.
Render out all these VST's to audio at 96K.
Down sample that rendered 96K audio now to 44.1 K again and drop them into your original session.
Compare them with the VST parts you renderd out at 44.1K and you will find often the 96K down to 44.1K versions sound better.
Any other way is not correct. There is no point in rendering out any audio from VST's at 44.1K then up sampling to 96K and back down again. Not sure of you are doing that but that wont work.
The idea is to get the midi parts playing these VST's right from the start at 96K. It is only the
Midi parts that allow you to do this only. You are not messing with the original session audio at 44.1K. Leave that all alone. The idea is to just remake any VST parts at 96K and down sample them back to 44.1K.