I have multiple pages that have unlinked elements from the original ones (e.g. navigation bar or footer).
This happened, I assume, because I duplicated a page. In this process, all linked elements were copied but lost their link to the original element.
Would be great if this could be fixed because it is very annoying to manually re-link all the elements!
I couldn’t reproduce this issue. When I duplicate a page with linked components, the links are copied correctly.
I would suggest you double check your work first. Then try doing a simple test with a new site… add a couple pages, create some linked components and then duplicate one of the pages. See if you can reproduce the problem. If you can’t, it may be that your bsdesign file has become corrupted. You could also upload your bsdesign file and someone here can take a look at it.
You are right, seems to work now! Is it possible through that some update broke existing links?
I was just going through all my pages and none of them had any link in them…
I’ve had some issues that I thought were the app with Linked Components, but then I found that for some reason, I had forgotten to link one of the pages and I just happened to be using that page to duplicate for other pages and never noticed it. Took me a bit to track it down, but check to see if that might not be what happened to you too.
The beauty of this app though is all it takes is to copy again from another page, paste Linked it back in and delete the unlinked ones and done. We don’t have to redo it all! Yaaaay! 
I’ve made the same mistake that @jo-r described above, and sometimes not noticed it until weeks later when I’d go to update something on a menu I thought was linked only to find when I’d check the live site, the change wasn’t appearing throughout the site.
I’ve never had an update break the linked components feature.