I occasionally come across this problem over the years, then forget how to solve it and scour the internet.
I am sure in the years since this you've figured it out.
I am currently working on a song that had several tempo changes. The band stopped at the end of each change with the idea that I could seamlessly merge them all together while mixing. Now of course, as I drag regions across tempo changes used for the metronome - the audio warps or goes out of sync.
I think I have once again "re-remembered" how to solve this, so I will type this response many years later to your query, partially so that the next time I search for this, I'll likely stumble across my own answer here.
What I did was select all regions. Then I dropped down the Region menu in my Arrange window and selected "Lock SMPTE position". This means the regions will not move if you now change the tempo. All I did then was straighten out the tempo automation so that the entire project was one tempo. Pretty sure I just picked a random tempo. The regions stay put because they're locked. After that, I pulled down the Region menu in the Arrange window again, and clicked "Unlock SMPTE position". Now I can freely move everything around the Arrange window unaffected.
Sorry for replying many years later - and to the me in the future looking this up again, you are very welcome me.