When scanning documents through a copier to email, the created emails with the PDF attachments are going to built-in Junk Folder. On the Exchange server I ran the following command in the Exchange powershell Get-OrganizationConfig and look for SCLJunkThreshold this should be set to higher the SCL value the scanned email is coming in as.
The email’s in the Junk Folder had an SCL value of 5, so I ran the following command to change the SCLJunkThreshold.
Set-OrganizationConfig -SCLJunkThreshold 6
Run another Get-OrganizationConfig and confirm the changes took effect.