With thunderbird open, select view settings for this account - click on Local Folders - look on the left pane and there will be a path to the local folder with a XXXXXXXXX.default file listed. This is the current profile that is being used by thunderbird.
Then look in C:documents and settings\username\Application Data\Thunderbird\Profiles - this is a hidden file so you will need to change folder options to show hidden files.
There is a Profiles.ini file - open with notepad and you will see it uses XXXXXXXX.default as the profile.
The quick and dirty way to restore the old emails is to drag and drop the old profile into the profile folder and the edit the profile.ini file to use the old profile.
If you google for profile manager for thunderbird there is an add on that handles multiple profiles and will start thunderbird with a different profile as selected by you.