Hello again.
I think I remember the details of your thread (maybe post a link to it so folks can access it from here).
IIRC you were stretching the performance using the Slip Stretch method I described (or maybe you changed to another method).
Did you use the "Bounce to Clips" action to bounce the stretched clips BEFORE comping the takes together or did you leave the stretches "active" and then somehow do your comp and use "Flatten Comp"?
45 minutes is WAAAAAY too long for either action so maybe if you did not "bounce" each of your stretched clips before creating your comp and/or went straight to "Flatten Comp" (not bouncing the stretched clips beforehand) the action is confusing Sonar.
Short version...
All the takes you stretched should have remained isolated from each other as you did your stretching (so each take matched the desired tempo BY THEMSELVES).
After all the takes were stretched to your liking each one should have been bounced individually (as in you would select all the clips in that take whether they had been stretched or not) and done a Right Click > Bounce to Clips action. That would bounce the stretches and turn all those split up clips into one single clip (this can actually be done on multiple tracks/lanes as well at once and provide one clip per track in a bulk process but let's ignore that for now).
AFTER you have done all the required stretching to get all you takes/performances to the timeline THEN you would make your "comp" across the takes (that now do not have any stretching applied and started off as single clips).
After all that is done THEN you'd youse "Flatten Comp" on each track.
Not sure if that's the problem but I'd imagine using "Flatten Comp" on a pile of stretched clips might try to do multiple actions at once and bork out Sonar so do it in stages.
I've never tested it though but definitely 45 minutes is way too long.
I will say though that when I do multi track stretching that involves lots of splits across all tracks that when I do a bulk "Bounce to Clip" procedure the processing takes quite a while. Like let's say 9 tracks with a couple dozen splits all stretched takes maybe 5-10 minutes.
I am however using an i7 desktop with 16GB RAM and 7200rpm HDDs. A modest system these days but still pretty powerful and fast.
List your system specs and provide some extra info based on what I described but I think if you do it in stages you'll get better results.
Cheers.