Check to make sure that your emails are going to your archive folder. Confirm that the emails are stored in the correct location. Troubleshoot the problem with the following steps:

1. Check account setting and the folder you want the email to be stored in.
2. Verify that your archive folder is not corrupted.
3. Re-sync your mail box with the help of your service provider.
4. Try deleting the email account and adding it back in.