why are some PDF's corrupted through Outlook, but fine with OWA? How to stop this?

Hard to say for sure but the first step would be to save (into a folder on the hard drive) the same PDF from both the desktop app and also from OWA and then start doing some comparisons.

1. Check the file size first. Are they the same or is the corrupted one really small compared to the working one?

2. Next, use a text editor like notepad to open up the PDF that doesn't work and see if the content looks like a normal PDF (you can do the same thing with the working PDF to see what it -should- look like) or if the content of the corrupted PDF is actually something like web page / HTML or an error message or something. (My guess is that you'll see something that clearly isn't a PDF).

3. If the beginning of the corrupted file looks like a normal PDF (looks like the  beginning of the working PDF) then scroll down to to the very end and see if there is anything at the bottom that might indicate an error or perhaps it was cut off. If it was cut off, then the exact size (in bytes) of the corrupted PDF might be very important.

4. Finally, if saving the files to the local hard drive results in two PDFs that are identical and both of them open up correctly, then that might indicate it's just a problem with the embedded viewer / plugin within desktop Outlook.

First item will be to define "corrupted".

Download the .pdf file out of your message, rename it with a .pdf extension if required, then open the file.

Provide 100% of the output produced showing "corruption".

Note: If you have some sort of scanner's running which are editing your message attachments, corrupting them, then you must turn off whatever scanner facility(s) you have running.

Some helpful data to explain the "corrupted" diagnosis:

When I open with Mac Preview: "The File "file name.pdf" could not be opened. It may be damaged or use a file format that Preview doesn't recognize"

When I open the same PDF with Adobe Acrobat Reader DC: "There was an error opening this document. The file is damaged and could not be repaired."

At this time there is no way for me to see any of the text on the document in question, to check if it breaks off suddenly or not.

This issue has not happened recently after I did a profile-recreation on the user's outlook application. Will update or open a new question of this issue persists.

Thank you both! 

It's easy for these questions to get forgotten and never closed  - can you close out this question and if the problem comes up again, open a new question?

Thanks!