If I make link changes in the prototype screen, the update link option doesn't appear until I close and reopen the document.
Sorry for the delay on this! As one of the other people mentioned, you can click on “Share Again” button to update your prototype. Please do file a bug if this doesn’t address your issue.
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Ulrik Groth-Andersen commented
True. You can however click "Share again" and then click "Update". But that's not very logical and could be made much easier/up front :)