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Your "Manage Third-Party Updates" menu did not make mention of any of those other sphere handbooks, so if your portfolio relies on information from those sources I would not be surprised to see those errors. If you have those packages I would go ahead and reinstall them. But instead of installing straight from a .hl file I would recommend you use the update process (detailed in the readme for each package) to grab the latest versions, otherwise you're likely to be in for another mess of errors from outdated files.
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