I have found that keynotes disappear most when using them in conjunction with dependent views. That's one of my biggest reasons for making dependent views independent after creating them.
I believe the dependent view issue is when you put the keynote close to the drawing split, you can fix this by providing wider overlap between dependent views.
I have seen this happen a few times on Roof plans, my hunch is that it is because of the view range as well as we like to show more than a roof and extend the view further down to the ground.
If you tag a pipe rise that goes beyond the view top or depth limits you can have issues for the same reason. The note doesn't know if it belongs on the level above or below. Sloped pipes similar. Just can't keynote those things. I have a dynamo script for placing tags automatically and going to rework it into a keynote script to autonumber notes as really what more do I want from keynotes