1.
Use the advanced filters to !EVTotal=0
2.
There's a new setting in the latest commits (since the last release) to bypass the "is present in current save" check.
https://github.com/kwsch/PKHeX/commit/5636e1ef4aa433122894b074d00cdf17b46c466a#diff-08cc001c6c0d5099a6160e2fd220324221b119ec147e29281352a64152874c61
Have you tried opening the edited save in pkhex after exporting it to check if the changes are seen by it? Did you make sure to click save in the items window?