Thanks DTLow and macfixer ! I already have Preview as my default for PDFs in Evernote. The problem is when annotating Preview makes a copy of the PDF and wants to save it on my Desktop rather than back into Evernote. So I have to then manually drag it back from the desktop and replace the previous PDF saved in the Evernote. I believe that Evernote used to work, and this is a bug that have crept back in. I'm running:
Version 7.9.1 (457703 App Store)
Editor: 62.3.7750 (ee6e44e)
on MacOS Mojave 10.14.4 (18E226)