The wand buffs don't work:

It works now, thanks for the help...
...
...
...
LOVE YOUR PLUGIN!

Can you please show me the /wand describe of that wand?
And how are you getting these protections, is it from your path configs?

I added them in the wand's yml file and it used to work in the previous versions, only after the update they stopped working. Also Using the buffs shop spell where you add those buffs to a wand, they do the same thing

Oh, ok thanks I bet I know what's up- they are working, but unfortunately they were changed in a way that break custom localizations.

If you have a wand.protection entry in your messages.yml, you will need to remove it. If you've customized all of the protection lore you'll need to re-arrange it a bit- the new config looks like this:

wand:
# .....
    protection:
      overall: "&2Protection $roman"
      physical: "&2Physical Protection $roman"
      projectile: "&2Projectile Protection $roman"
      fall: "&2Fall Protection $roman"
      fire: "&2Fire Protection $roman"
      explosion: "&2Blast Protection $roman"
      magic: "&2Magical Protection $roman"
      unknown: "&2$type Protection $roman"

This was done to support custom protections with custom damage types. I'll bet you have something like protection: "&2Protection $roman" in there, which is breaking things because it expects a whole section now instead of a single string.

A regrettable change in retrospect, but that's progress I guess.

Will the messages.yml regenerate to its updated version after a server restart if i delete it?

If you haven't put any edits in there you can delete it. But in that case you shouldn't have copy+pasted stuff into it in the first place ....

None of those files regenerate, it's kind of not how the plugin works. You're meant to put your changes in your configs, and let things you haven't changed update when the plugin updates.