I have two Thunderbird (5.0) Portable instances on Windows 7:
How can I import mail folders from one into the other?
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You just need to copy the full profile between both instances, then select the profile you want to use with:
thunderbird -P [profile]
if you omit "profile" the graphical profile manager will ask you which profile you want to choose.
If you just want to overwrite one profile with the other, just remove the one you don't need.
Chech the following link to locate where are your profiles; you haven't said which OS are you using: