At a glance it looks like the problems concerning bi-directional notes are solved.
A few more observations
Search queries are not highlighted past the first match (i.e., after a Search Next command all instances of the found string will not be highlighted including the first instance)
Nothing happens after clicking an intra-collection link (i.e., Wikilink, Backlink, etc.) to a note that does not appear in the Found notes list
Would it be a good idea if the Notes list “reset” to list the entire collection, the search bar remained populated with the last query (as is the norm already it appears) and the previously unfiltered note was selected and displayed?
Successive Search Next/Previous commands can then behave like a normal search (i.e., navigate and display notes + search matches without re-filtering the List pane)
I recommend the above because it looks like whether a note can be displayed depends on it being selectable in the notes list
I’m still thinking about how to handle your second observation, about the problems related to found notes linking to non-matching notes. I may need to ponder on this a bit. But you raise a good point!