Thank you, 273,
Your idea works perfectly!
I did this:
As per the instructions in the link, I copied my profile and my local mail folder to a separate directory on an ntfs partition I had, and pointed the ./.thunderbird/profiles.ini file to the same. Then, I copied this ini file to my other OS. Now, Its as if I am opening the same mail client no matter which OS i am on!
cool! It prevents repetitive downloading of same mail, and missing mail!
Thank you once more!