Not sure if this helps but...
Assume you have a project with plugin X in use on some track. For some reason that plugin goes missing or gets uninstalled. You open the project at a later time and you'll see the message you quoted in the FX chain about the effect missing but the configuration is preserved.
So you reinstall the plugin, have reaper rescan VSTs and it finds it just fine, however when you return to the project and that track's FX chain, reaper for whatever reason didn't reassign that saved configuration to the plugin and fix things.
What I have successfully done in the past is to select that plugin in the FX chain, CTRL+C to copy it to the clipboard, then immediately CTRL+V to paste a copy of it into that same chain, this should force reaper to link it back up to the working VST then you can delete the failed instance.
I've not tested this fully such as confirming the FX params were all properly restored but it did proverbially work and got me out of a tight spot with an old project where I had deleted the VST because I forget I had used it.