I'm assuming this isn't one of the system mailboxes (In, Out, Trash, Junk).
If you let one of those get that big, you would really be asking for trouble!
Personally, I wouldn't let any mailbox get that big.
Do you have a backup of the data folder from before the improper closing problem happened?
If you rename the present folder by adding .old to the folder name, and put the backup in its place, does the error message still appear?
If so, it doesn't look like the bad close-down of Eudora caused it.