I've encountered it before where I KNOW I've made notes on particular players only
to NOT see them the next time they were on my table. Not 100% sure what that was all about but I contacted Pokerstars about it,.. they asked me to forward my notes files to them (I didn't want to so just experimented a bit with it myself).
Seems I need to shut my computer down in order for all my 'new notes' to stay saved on file (I clean my puter out often,.. due to some poker programs I run on it while playing and FILLS up my files real fast).
Since shutting down puter after a session each time, I've never lost another note to my knowledge.