Sequence:
1. In the last stable version I created a Lector's Palette and used it to mark Colossian 3:1-11 as a proof of concept
2. Note file of Lector's palette was created in the beta version
3. Tonight in 4.5 beta 12 I added one style
4. I applied 1 highlight on Genesis 15:1-21:3
5. I manually added a note (Feast of the Holy Family)
6. I tried to delete the Colossians proof of concept entries - could not get the red x
7. I went and selected the Colossians passage and used the erase function. This removed the highlighting but did not remove the notes.
8. This is the point I took the screen shot. Now that the highlighting is removed the red x for deletion is available.

I'm going ahead and deleting the dead entries and continuing with the work I intended to do. Obviously, it's not easy to reproduce the conditions but I'll let you know if I find repeats.