Restoring compacted emails

This is more to do with Thunderbird itself, not the portable version, but a brief look on Google brings up this

Undoing compacting

You cannot undo compacting, there is no such thing as "uncompacting". Compacting physically removes messages marked for deletion and hidden from view. Once they're gone, they're gone. Usually when somebody asks how to "uncompact" a folder they lost messages due to compacting. Sometimes the messages were already gone, but that wasn't noticeable because they were still listed in the folder listing. Other times compacting a folder physically removed messages it shouldn't have because the folder was too corrupt.
If you suspect a folder is badly corrupted, don't compact it. It might make things worse because compacting depends upon Thunderbird being able to parse the mbox file (the text file named after the folder that contains all of the messages for that folder) and figure out where every message begins and ends. Thunderbird can't use the so-called index file (folder_name.msf) to do this. Once Thunderbird starts to lose track of where each message begins and ends, compacting can cause the physical removal of other messages because it thinks other messages are part of the deleted message. It's unusual but possible to lose every message in a folder by compacting it if the folder was badly corrupted.

from the mozillaZine article on compacting folders.