You cannot open PDF files directly to Adobe Reader due to Adobe not releasing their API to Intunes SDK

Workaround : 

• Add Adobe Reader to Protected Files in your MAM policy
• Install Microsoft Onedrive on the device
• Download the file \ Attachment ( It will download it to Onedrive secure area ) 
• Open it with Adobe Reader

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GPO  Set a default associations configuration file under Computer Configuration > Administrative Templayes > Windows Components > File Explorer

Save the follwing file as an XML and use this

<?xml version="1.0" encoding="UTF-8"?>
<DefaultAssociations>
  <Association Identifier=".acrobatsecuritysettings" ProgId="AcroExch.acrobatsecuritysettings" ApplicationName="Adobe Reader" />
  <Association Identifier=".fdf" ProgId="AcroExch.FDFDoc" ApplicationName="Adobe Reader" />
  <Association Identifier=".oxps" ProgId="Windows.XPSReachViewer" ApplicationName="XPS Viewer" />
  <Association Identifier=".pdf" ProgId="AcroExch.Document.11" ApplicationName="Adobe Reader" />
  <Association Identifier=".pdfxml" ProgId="AcroExch.pdfxml" ApplicationName="Adobe Reader" />
  <Association Identifier=".pdx" ProgId="PDXFileType" ApplicationName="Adobe Reader" />
  <Association Identifier=".xdp" ProgId="AcroExch.XDPDoc" ApplicationName="Adobe Reader" />
  <Association Identifier=".xfdf" ProgId="AcroExch.XFDFDoc" ApplicationName="Adobe Reader" />
  <Association Identifier="acrobat" ProgId="acrobat" ApplicationName="Adobe Reader" />
  <Association Identifier="http" ProgId="IE.HTTP" ApplicationName="Internet Explorer" />
  <Association Identifier="https" ProgId="IE.HTTPS" ApplicationName="Internet Explorer" />
</DefaultAssociations>

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A user was experiencing this issue. Forwarding the email back to the user and another user showed the attachment fine.

The attachment showed on mobile devices/webmail and also via a third party Outlook Attachment Add in

Looking at the headers of the email the Mime type was multipart/alternative this should be encoded to multipart/mixed

multipart/alternative is for sending text/html and text/plain versions of a message, and multipart/mixed is for adding attachments.

1) Speak to user sending mail to find out why emails are being sent as multipart/alternative

2) Create a hub transport rule to re-write multipart/alternative to multipart/mixed

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