If your email application supports it, you should periodically compact your mailboxes.
Some email programs like Thunderbird and Eudora maintain your mailboxes as efficiently as possible by temporarily recording updates at the end of each mailbox file, instead of performing edits like additions, moves, and changes within the mailbox each time. These programs then have an option to “compact” the file to work in all the edits at one time (Thunderbird: File / Compact Folders; Eudora: Special / Compact Mailboxes).
If your computer crashes in the middle of a mailbox operation, and your mailboxes haven’t been compacted in awhile, the settings that keep track of the updates can get lost. When this happens, you can find that deleted messages have been restored, messages long moved are still there, and other updates since the last compact operation have been lost. While this is rare, to protect against it and keep your files in good order you should compact your mailboxes about once a week, or after any significant set of changes. Compacting your mailboxes also saves some disk space, and could make your program run a bit faster.