I recently updated my Kontakt portable plugin and Reaper is seeing it as a different plugin (vst3) so basically all my previous plugin settings from my projects are gone. Is there a way to resolve this? I deleted the old one without saving any presets so this could be an issue.

 

Not sure what you are upgrading from. You can just keep older versions of Kontakt around. I have 5, 6 and 7 installed in parallel. VST2->VST3 has no reliable upgrade path. 6->7 can be seamlessly upgraded, but only if both Kontakt versions were using VST3 in the first place and only if the DAW supports VST3 migration, which Reaper doesn't - as far as I remember.