I have created an isolated group for this issue:

  test:
    permissions:
    - -vanish.effects.lightning
    - -vanish.effects.explode
    - -vanish.effects.smoke
    - -vanish.effects.flames
    - -vanish.effects.bats
    - -vanish.effects.toggle.all
    - vanish.*

This is using PermissionsEx v.1.20.4

It would seem after running "/pex reload" and "/vanish reload", that the effects are still enabled on the users that previously had effects. The reload states it reloads the VanishUsers, however looking at the reload function that the reload command calls, I see no refreshing of the user files, so I would believe it isn't resetting the boolean values in those user files:

https://github.com/mbax/VanishNoPacket/blob/master/src/main/java/org/kitteh/vanish/VanishPlugin.java#L359

Shouldn't those checks be dynamic? As far as I can tell from testing, the user files are not refreshed with "/vanish reload". It just simply prints that they are. Seeing how .getUser() works, it would seem you could also just dump the map entirely as well on a reload.

Any node that defines the on-join state of a toggleable feature (Such as the effects, but also including nopickup and other prevention-of-interaction stuff) is pretty much just reloaded on quit/join.

Also, why not just grant vanish.standard and then add the nodes you want instead of starting out with EVERYTHING including the questionable vanish.silentquit node?

I see, so to truly reload a specific user they need to relog. I suppose that works.

As for the nodes themselves, we actually wanted the specific ones '*' granted, it was only the loud effects that were a bit of a downfall. I read the documentation beforehand :p