Ugly as it may be, using Lightroom as the core of the workflow frequently requires adding and removing images from the database. An efficient workflow provides for this and ensures that *most* of your work will remain intact.
Maybe Optimizing will fix some of those corrupt records.
In any case, based on my past experience with various databases, if you've got bad data in there you often have to recreate those records one way or another; there may be no way to "fix" it. But the files themselves should be safe if you've saved everything along the way.
Admittedly, if you have 9 images showing in the Missing Files collection, it's probably not a big deal to remove them and re-import. If you have thousands images showing as Missing, you've got bigger problems and the database really needs attention.
Maintaining a clean LR catalog takes persistent work. I take it for granted that I might have to redo a few things along the way. Ugly workarounds are sometimes the prettiest solution in a production environment.