If something got blacklisted, it’s either a redundant plugin (like a VST2 version of a VST3 plugin) or something that seriously misbehaved during scan. Go to the blacklist tab and click reactivate on the plugins that you’re sure aren’t just redundant VST2 versions.
If they’re sent back to the blacklist, then there’s something wrong with the plugin and you’re supposed to investigate. Check if there are any updates, and/or try to reinstall the latest version.
Comments about Cubase being unstable have basically disappeared since the blacklist was implemented. I know it can be annoying to have plugins blacklisted, but this is all done to save you a headache in the long term. It’s better to have to troubleshoot a few plugins once than trying to figure out which of your 50+ plugins are making a huge project crash.