Had a hard time labeling this, so here are the steps:
Open Bible, mine is the ESV and open the TOC and click on the notes icon:

Just learned this was here and it is very helpful!
Now select a book of the bible from the notes menu, I picked Romans:

Here are all my notes in Romans. So good so far.
Now clear the notes by clicking on all in the notes menu:

The menu shows all my notes again, but the Bible text is still filtered. I had to close the ESV and reopen it to get back to the complete text.
So either I am missing something or this is a repeatable bug.
L8 Mac SR2
MBP High Sierra
Thanks