Just one more Evernote/Penultimate customer registering my frustration with this bug. When I inquired via customer services several months ago, I was told that this was a known issue that they were working to solve. Now that I see the length of this topic thread, I have my doubts that anyone cares to fix it.
I'm an Evenote Premium paying user (since 2011) and four things about Penultimate/Evernote have pushed me toward other note-taking apps on my iPad Pro.
1. This bug which seriously degrades Penultimate's usefulness for taking, editing, and organizing hand-written notes.
2. No ability to capture audio while taking notes.
3. Not optimized for Apple Pencil which leads to lots of stray dots and lines from my hand resting on the screen.
4. Inability to add photos to Penultimate notes while taking notes on the fly.
So, it seems like a slow motion race to me. Will Evernote address the issues above before a very notable competitor adds keyword searching of hand-written notes? The competitor has the 4 issues above solved. Evernote has only their strong searching capability to keep me using it. Whoever puts it all together first will have the winner and the other one will fade away.