The Message Archive facility is for VPOP3 to store copies of all messages sent or received. It stores the messages in a central archive store which can be searched by an administrator. The prime purpose of the archive facility is for recording messages in case of possible disputes, as you can see what was sent/received by email. It can also be used as a backup/restore facility in an emergency, but that is not its prime purpose, so it is better to have a proper backup facility as well.
To enable message archiving, simply go to Settings → Message Archive in the VPOP3 settings and check the Archive Messages box, then press Submit
When messages are sent/received, then the messages are stored in the VPOP3\_archive folder (not subfolders) as P<something>.DAT. At this point the messages are not indexed, and cannot be searched.
Later, a background thread will detect the P*.DAT files and read them, insert the data into the searchable index database, and move the file to a subfolder of the Main Archive Store folder (which may be VPOP3\_archive, or may have been changed) and renamed to A<something>.DAT. At this point the message is indexed and can be searched for.
If the index database is lost or corrupted somehow, then you can force VPOP3 to reindex the messages by moving the files from the Main Archive Store subfolders into the VPOP3\_archive folder (not subfolders) and renaming them to P<something>.DAT (this is most easily done from a command prompt (eg REN A*.DAT P*.DAT). After a few minutes VPOP3 will detect these new messages and start indexing them. This may take some time if you have lots of messages. Assuming you are using a recent version of Windows you move & rename the files with a few commands in a command prompt (CMD.EXE) window:
C: CD \VPOP3\_archive FOR /D %i IN (*) DO MOVE %i\A*.DAT . REN A*.DAT P*.DAT
If your VPOP3 is not installed in the C:\VPOP3 folder, then you will need to change the first two commands as appropriate
(make sure you have a backup first)