I haven’t received any correspondence from Evernote about this issue other than them saying they know it’s an issue.
My best advice is to ditch Penultimate. Evernote obviously don’t care about providing a robust note taking application, otherwise they would have fixed this issue by now.
For reference, I now use Goodnotes and absolutely love it. It has much more capabilities than penultimate and with their auto backup feature I basically have a constant up to date pdf copy of all of my documents on the cloud for access at any time.
The iCloud sync function does struggle once you get over a certain size in your documents but it’s not a critical part to the apps function when you can still back up manually and also have it export a updated pdf for all documents automatically.
The pen isn’t as good as penultimate but that fact that the app works outways this issue for me.