agreed, bounce em all to clips. this happened to me when i had finished sinking up the bass guitar and drum transients. when i finished i bounced just the tracks that i had played with the timing of, and kept getting that message when i would try to save the program as a bundle file. it ended up working only after i highlighted all 48 tracks, and bouncing to clips, not just the 9 tracks i messed with the transients on.

Don't save as a bundle!

Save as a normal cwp.

If for some reason your cwp ever becomes corrupted, you can, theoretically rebuild in from the wavs stored on disc which will not be corrupt.

If for some reason your cwb ever becomes corrupt, that's it, game over, you've lost everything in that project permanently