I imported a bunch of stems and did a ton of work in a project.  I then realized I forgot to set the tempo before importing so the project was set at the default 100bpm.  I now want to change it to 88 but when I do all of the clips warp and the song sounds way off.  Is there a way to just change the tempo ( I want the measures to line up) without affecting the audio?

Absolutely!  The only time your residing audio would be affected by a tempo change is if it were an acid or groove clip.  So, the audio (transients) will all stay as originally recorded or imported regardless of the tempo change or tempo of the new project.
 
Kind regards,
 
tecknot

They don't though. I don't have any groove clips in this project and all of the tracks move after typing in a new tempo.

Audio tracks will appear to change length because the M:B:T grid is the absolute visual reference, but they will play back the same.
 
The only thing that will cause an issue are clips that don't start at 00:00:00:00. This is because the default timebase for both MIDI and Audio is MBT, so their start times are locked to measures. You can change all their timebases to Absolute, but the easier way is this:
 
- Snap the Now cursor to the beginning of the measure corresponding to the Current Tempo + 1 (101 in your case).
- Hit Shift+M to open the Set Measure/Beat At Now dialog and enter Target Tempo + 1 (89) as the measure, and OK.
- SONAR will change the initial tempo to make the timeline hit that mark at that absolute Now time without changing the absolute timing of anything (including MIDI if any).
- In case you're wondering, the "+1" is needed because measures are counted from 1, not 0.
 
 

headsnack
I imported a bunch of stems and did a ton of work in a project.  I then realized I forgot to set the tempo before importing so the project was set at the default 100bpm.  I now want to change it to 88 but when I do all of the clips warp and the song sounds way off.  Is there a way to just change the tempo ( I want the measures to line up) without affecting the audio?

 
Assuming you have many individual clips on each track (slip edits). 

Select all. Bounce to clips. This will create continuous clips per track. Now, drag all clips to start on any measure's beat 1 (but all on the same measure, beat 1). Select all again. Bounce to clips again. Change tempo.
 
Simples.

2 Completely different ways, both of which work perfectly
 
Good work men!

Thanks so much to everybody!  I honestly prefer the first method of changing the measure.  Even though an audio bounce should be clean, I'm always weary of having multiple tracks of bounced silence in my compositions. 

headsnack
Thanks so much to everybody!  I honestly prefer the first method of changing the measure.  Even though an audio bounce should be clean, I'm always weary of having multiple tracks of bounced silence in my compositions. 

Understood.