For anyone that used Evernote as a "Document Storage" app instead of just purely notes, I found Notebooks, https://www.notebooksapp.com/, https://www.notebooksapp.com/ to be a good replacement.

It works with files on your harddrive and your existing cloud storage (icloud / dropbox.) macOS/iOS only, but for someone who primarily is storing PDFs this was a much better fit than more alternates that are for taking notes.