I checked the version of Zotero on my iPad and despite being the updated one, I saw all the annotations from a pdf disappear right before my eyes about 10 mins ago.
I have version 2.0.4. I didn't find the annotations on my desktop version and when I reopened the Zotero app on my iPad which was open in the background, the annotations that were there on the screen disappeared as the PDF was reloading.
That just means you were still using the earlier version with the bug earlier today when you created the annotations, so they were never saved correctly. (Our server logs confirm that.) The app then updated, but unfortunately that won't restore the previous annotations. This won't happen again going forward.
Upgrade Storage
When you say they disappeared right before your eyes, what do you mean?