Please specify if the database is the server replica or a local replica of the mail file.
It would be a good idea to check the all documents view to verify if the documents are visible.
Are there any backups available of the mail database? If yes you can run show database on the server and compare the results that you have with both of them.
The documents count difference can be still down to deletion stubs since they are not copied over to new Notes copy but would be copied to the new replica. Running "show database databasename.nsf" would provide you with that information.
Looking forward to hear back from you.