Well, the first thing you should do in this instance is check if Reaper attempted to load the plugin when scanning for new plugins.
Options->Preferences->Plug-Ins->VST.
Single left click the re-scan button. Hover over "Plug-ins that failed to scan". Are the plugins "that won't show up" showing here?
If no, then the problem is almost certain to be that you don't have the path to appropriate the plugin file set up. That's that first text box in that preference window from above.
If it DOES show here, then there's appears to be something wrong with the plugin itself that caused Reaper to be unable to open it. This happens from time to time, and unfortunately can be tricky to figure out. In that case, it's probably best to specify which plugins you're having trouble with.
In that aforementioned "Plug-ins that failed to scan" preference, you can actually click on any line in there and Reaper will attempt to reload that single plugin. If you're lucky, it will just work. If not, when, then there's troubleshooting to do.
You could also do a "Clear Cache and rescan" (click the Re-scan button and then that option), but this will re-scan all of your plugins and can be a slow process.
FYI, the file reaper-vstplugins64.ini is what holds all the VST/VSTis that Reaper found, whether successfully loaded or not. You *can* edit this, but you should make a backup of it first if you do (although you can always regenerate it with a Clear cache/rescan)... but really I don't think this is going to be what will fix the problem for you.
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