So I've been using this for a checklist as I work my way through the game (I'm at the Yureyu battle right now, so pretty much at the end of what you have), and these events all seem to have changed/been removed:
Tynamo in Peridot Alley (can't remember if Pokemon just changed or none there at all)
Electrike in Obsidia Ward
The caged Nidorina in Rhodochrine Jungle (couldn't find)
Heatmor in Pyrous Mountain (not there)
Finding Cain's earring on Azurine Island (doesn't happen)
Might I suggest also adding a list of things you can go back to do once they become available, or at least a "come back once you [whatever]" note? Like, there are about three or four different events in Citrine Mountain that you can't do while you're actually in the area, but they're worth coming back for later - the Beartic battle is unwinnable when you're there the first time around, once you beat Aya and can use Strength outside of battle you can get the TM for Double Team, and Corey's Croagunk is waiting there for something like it's an event Pokemon but you don't have whatever it is you need to get Croagunk to join you.