Similar problem happened on my Lazarus-Linux several times. After OS upgrade and reinstalling Lazarus, some previous installed packages did not work. Because those packages were already there, so I tried to rebuild the IDE, unfortunately Lazarus failed to rebuild.
My solution is manually remove those problem packages, rebuild the IDE and reinstall them back (using Online Package Manager).
So, I think you may be able to fix your issue by rebuilding the IDE. If it fails, try to uninstall those packages. If you cannot uninstall them, you can force it by deleting the files. After that, rebuilt the IDE and reinstall the packages.
This trick works on Linux, it may also work on Windows I believe.
-edit-
Sometimes I remove the config files before reinstall the IDE, to trick it to threat it is as a fresh install. But because I want to keep some config settings, I usually manually remove some lines in the packagefiles.xml.