I have the exact same problem on an iPad with a pdf file annotated outside Zotero, then added to my Zotero collection. When I open the pdf file in Zotero on the iPad (Zotero version 1.0.3), the annotations are not visible. When I open the file in Zotero on Windows 10 (Zotero version 6.0.9), the annotations are there.
It's not the same issue — the other thread was about a third-party plugin, not the Zotero iOS app. I've moved this to a new thread.
If you're using a PDF reader that saves annotations back to the file, they'll be visible in the built-in PDF reader in the desktop, in the web library, and in the iOS app as long as you're syncing files and file syncing is working correctly. Zotero on the desktop will detect the change and upload the file, and the iOS app will download it.
But if you're saying you've configured desktop Zotero to open files in an external PDF reader, rather than using the built-in PDF reader, your PDF reader might just not be saving annotations back to the file (e.g., it might be using some separate file).
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When I open the pdf file in Zotero on the iPad (Zotero version 1.0.3), the annotations are not visible.
When I open the file in Zotero on Windows 10 (Zotero version 6.0.9), the annotations are there.
If you're using a PDF reader that saves annotations back to the file, they'll be visible in the built-in PDF reader in the desktop, in the web library, and in the iOS app as long as you're syncing files and file syncing is working correctly. Zotero on the desktop will detect the change and upload the file, and the iOS app will download it.
But if you're saying you've configured desktop Zotero to open files in an external PDF reader, rather than using the built-in PDF reader, your PDF reader might just not be saving annotations back to the file (e.g., it might be using some separate file).