The installer contains updates not just to the main program, but also to the add-ons. so even if you have the latest program version, there will still be things in the updater that updates the add-ons. This is why it should be run at the end after installing everything.

What do you mean when you say things are gone though? Is it replaced by red X'es, or just completely gone? If it is the former, it means that you are missing art resources you used to have installed, which probably means you forgot to install something on your new install.

And here's @Maidhc O Casain's entry added to the atlas:

Probably just the arrow head being tiny. Use Tools -> Set Properties -> Arrow Style and change it to something more reasonable for your map size.

Change the line width of the entity to 0.

Great. Means your issue is caused by the bug I stumbled over. Turns out notes also live on a sheet, so if you accidentally delete the one they're on (which there is no way to tell) you also delete the notes. Seems like they're on the LAND sheet for lot of the official templates (by pure coincidence), but no guarantee all templates are like that (probably not, since city and dungeon styles don't have a LAND sheet at all).

I've reported this to the appropriate authorities.