I also meet a similar problem. The annotation or highlight will disappear I added on Z6 when I open the file in other PDF readers.

An additional issue related to this, is that the underline I made in other PDF reader (my case: foxit reader) appear as highlight in Zotero PDF reader.
I don’t want this because of my own distinction between underline and highlight when reading.

It will be great if you can fix this! ^^

I think that the choice to save PDF annotations in the database is based on solving real problems, especially with multiple editors, but it does create quite a bit of friction for those of us that would like to freely bounce between different PDF readers (all of which, in my case, save annotations to the PDF file directly).

Zotero offers workarounds with "Import annotations" and "store annotations in file", but they are clunky and manual. An improvement that I'd like to see is to offer the user a choice (and maybe this could even be offered as an add on or plug-in) to do this automatically when editing and then closing (and perhaps this wouldn't be available in the case that the PDF is shared with a group, to avoid that conflict). Also, it would be much better if those commands were exposed with keyboard shortcuts. Lastly, it would super if I could "flush" internal annotations en masse, by selecting all the items in a collection, and running a command to store annotations in the file.

The issue that we cannot see internal annotations in other PDF readers magnifies when we use Zotero on IOS. In this case, annotations we made on IOS with zotero internal readers, will not show up if we open in other PDF readers on desktop. Thus we are forced to use Zotero internal PDF reader if we need it cross-platform. I tried to use the internal reader, but it lacks many basic tools.
I hope this issue can be fixed soon, then Zotero is almost perfect in my view.