I have the same issue, though with a different editing program. On desktop I use Xodo to edit evernote PDFs, and it works perfectly. But on android even if Xodo notifies me to say my changes have been saved when I open the pdf again from evernote my changes are gone.
At the moment I either "save as" edited PDFs to my phone or I work on the files in Google drive (which does save changes as long as I have internet when I close the file) and reupload them to evernote when I have the time.
But a fix for evernote or a different app that works better with evernote would be ideal.