cms bin folder

When you applied the hotfix, did it properly update the /LIB directory for the CMS? I'd start there and see what the version numbers are. Technically speaking, when you build the CMS, it copies the /LIB directory files into the /CMS/bin directory. So if you did a clean or rebuild, that should clean the CMS up assuming your /LIB directory has the proper files in it.

For the MVC project, simply referencing the proper nuget package and rebuilding will resolve that issue.

Sorry, i was jsut speaking about the CMS for this, and the difference between what was on the live server (which was at version like 83) and now my local which is at 95. The bin folders are very different with the live site having a bunch of files the local doesn't. So I wasn't sure if I should just delete the live bin or just add to it?

hope that makes more sense

There are quite a few changes but the main thing is if you do a build/rebuild locally and you can get the CMS to run, you should be good. Regarding production, I'd just take a copy of the bin directory with all those other dlls in it and keep it for safe keeping in the event you have to roll back.

Short answer: yes

I always delete the bin and the obj after any Hotfix or Upgrade. Make a backup before doing this! A standard Kentico installation doesn't have any problems when you delete the bin and the obj folder.

Doing a "Rebuild" in Visual Studio is a Clean + Build. Clean will clear out generated files in the \bin and \obj directories.

Since these folders should always be excluded from source control, they can be deleted (manually or by running a "Clean" on the project) and regenerated just by doing a Build.