Archiving Email using Folders

Hello all,
I’m currently in the process of archiving email messages for users that have left to a folder on the system.

This works really well, however I have a user that has over 30,000 emails that I need to move across, however when the process is finished there are only around 23,000 emails showing in the folder.

Has anyone using this method come across this before, is there a way I can ensure all emails are copied over?

Thanks Helen