Is it possibly you accidentally made those WAV file groove clips ?
I would use the "Bounce to clips" function on all your exported files (Wave and midi)
A few other tips:
- Any tracks that have multiple clips in them, bounce them to 1 solid clip (using the Bounce to clips function)
- Make sure all your wave files start at 1:01. if need be, drag out the beginning and "Bounce to clips".
- Place a dummy notes at 1:01 on each individual midi track. then Bounce to clips. this helps with lining up your tracks
correctly. Because by default Sonar begins/starts a Midi clips where the Data starts. not at 1:01.
If all this is done correctly, your project should follow tempo changes as you have made them in previous projects barring you have the tempo changes in the correct places.