Thanks, when I tested this, with exactly your small PGN snippet, what I found is that only moves that overlapped with other repertoires kept the arrows. So I loaded the PGN you showed in your post , and then deleted that repertoire (then did a page reload just to make sure any in-memory arrows were also cleared - this step may not have been necessary, but I just wanted to make sure), then loaded a modified version of your repertoire with none of the arrow annotations, i.e this:
[Event "E5 Repertoire"]
[Site "?"]
[Date "2024.04.13"]
[Round "?"]
[White "1) 1.e4 e5 - Weird tries"]
[Black "2.Qf3 #1"]
[Result "*"]
1. e4
1... e5
2. Qf3 $6
2... Nf6
{ Best move}
3. g4 $2
{ Too stubborn}
3... d5 $1
{ playing for the centre. }
4. exd5 Bxg4 5. Bb5+
5... Nc6 $19
{ develop with every move}
*
At that point 1.e4 and 1.e5 arrows/colours had survived, as I still had those moves in other repertoires, so the delete repertoire would not have removed them (in fact there was a bug where these moves didn't show their arrows until after I reloaded the page, so it seems for overlapping moves to get their arrows a page reload was required, a bug which I've filed a todo list item against in our bug tracker). However none of the subsequent moves from 2.Qf3 onwards had arrow or square highlights shown.
So when you loaded your new repertoire, I assume you had cleared all the arrow/square annotations from the PGN as in my example above? Are you sure the persistent annotations were not from overlapping moves in other repertoires? i.e did the deeper moves in the repertoire that were unlikely to overlap still have arrows/square highlights?