EndNote Desktop corrupting PDF files

I recommend contacting Tech support but they will want to know: what Operating system and what version of endnote?  

Have you ensured you have updated/upgraded endnote to the most recent version?  (X8.2) 

If that does not help then:

I recommend that you contact Technical Support directly

1-800-336-4474 option 4 then 1 or

https://support.clarivate.com/Endnote/s/technicalsupport?language=en_US