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A couple of thoughts:
1. Try resetting LR's preferences:
https://www.lightroomqueen.com/articles-page/how-do-i-reset-lightrooms-preferences/
LR sometimes soils its preferences file, and resetting it can fix all sorts of wonky behavior. That article explains how to restore the old preferences if resetting doesn't help.
2. Use the free trial of the Any Filter plugin to see what the catalog internally reports for the presence of the smart previews. Select the built-in collection Photos That Failed To Build A Smart Preview, run the Any Filter > Filter command, click the magnifying glass, and select the Has Smart Preview criterion:
If Any Filter reports that all those photos in fact have smart previews, then the problem is just that the built-in collection isn't getting updated. But if Any Filter reports that those photos don't have smart previews, then the problem is more serious.
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This error is coming from LR internals, not the Any Filter plugin itself, strongly suggesting a catalog inconsistency. It's tempting to ignore inconsistencies, but that portends danger down the road.
I've never seen that special collection, Photos That Failed To Build A Smart Preview. I tried to provoke it by changing the permissions on the catalog subfolder "<catalog> Smart Previews.lrdata". LR then displays an error dialog when it fails to build smart previews, but it doesn't create that special collection.
It may be that this special collection is used so infrequently that's it's never been thoroughly tested by Adobe, and the problem could be simply in how that collection is built and accessed by LR, not affecting the rest of the catalog.
You could try Johan's suggestion of exiting LR, moving "<catalog> Smart Previews.lrdata" out of the catalog folder, restarting LR, selecting the special collection, and then doing Library > Previews > Build Smart Previews. If the special collection goes away, then I think you can rest easy. If it doesn't...
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I opened the .lrcat you sent and poked around a bit with my plugins and didn't notice any inconsistencies other than that special collection Photos That Failed To Build A Smart Preview.
With respect to that special collectioin, the last 65 entries in that collection are completely bogus and causing all sorts of errors when you try to use them via the LR app or access them via plugins. Clearly a LR bug somewhere.
I was able to delete the special collection by right-clicking it and doing Remove This Temporary Collection:
After removing the special collection, I recommend going through the procedure again of removing existing smart previews and building new ones (exiting LR, moving "<catalog> Smart Previews.lrdata" out of the catalog folder, restarting LR, then doing Library > Previews > Build Smart Previews). I'm not able to try that because I don't have access to the actual photos.
If building smart previews produces errors, be sure to grab screenshots of any error messages.
And does the special collection come back, and does it again have bogus entries at the end?
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With respect to the other issues you saw with the Metadata browser in the Library Filter bar, I'm not seeing those when I open the catalog:
After deleting the special collection (see above), are you still seeing this problem with the Metadata browser?
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