The attached patch series should fix this bug.

Patch 1:

     ert-x: New `ert-with-test-buffer-selected' convenience macro

     * lisp/emacs-lisp/ert-x.el (ert-with-test-buffer-selected): New
     convenience macro that extends `ert-with-test-buffer' by displaying
     the test buffer in a temporary selected window.  This makes it easier
     to simulate user input in the body via `execute-kbd-macro'.
     * test/lisp/emacs-lisp/ert-x-tests.el
     (ert-test-test-buffer-selected/*): Add tests.

Patch 2:

     ; whitespace: Delete unused `whitespace-font-lock-refontify' var

Patch 3:

     ; whitespace: Use `defvar-local' for buffer-local vars

Patch 4:

     ; whitespace: Fix indentation

Patch 5:

     whitespace: Reset `whitespace-buffer-changed' when refontifying

     * lisp/whitespace.el (whitespace-post-command-hook): Add missing reset
     of `whitespace-buffer-changed' back to nil between commands.

Patch 6:

     whitespace: Include empty final line in BoB empty match

     * lisp/whitespace.el (whitespace-empty-at-bob-regexp): Include any
     last line trailing whitespace in the BoB empty line match to ensure
     that those characters get highlighted.

Patch 7:

     whitespace: Redo BoB/EoB empty line highlighting

     * lisp/whitespace.el (whitespace--empty-at-bob-matcher,
     whitespace--empty-at-eob-matcher, whitespace--update-bob-eob,
     whitespace-color-off, whitespace-color-on,
     whitespace-empty-at-bob-regexp, whitespace-empty-at-eob-regexp,
     whitespace-looking-back, whitespace-post-command-hook): Redo the
     `empty' line highlighting logic to ensure that a buffer change causes
     all affected `empty' lines to become (un)highlighted (bug#37467).
     Also, for improved UX, don't highlight BoB empty lines at or below
     point (not just when point is at 1), or EoB empty lines at or above
     point (not just when point is `eobp').
     (whitespace-bob-marker, whitespace-eob-marker): Clarify documentation.
     * test/lisp/whitespace-tests.el (whitespace--with-test-buffer,
     whitespace--fu, whitespace-tests--empty-bob,
     whitespace-tests--empty-eob): Add tests.