One of the druid spells removes a rogues perks, namely Arcane Trickster (including saves/abilities etc.) I think he maybe Vine Mine but this is perhaps worth a look.
What makes you think so? One of the reasons the perks are as they are is to prevent all spells from removing them. The icons for the effects can be unreliable, going away when they are still in effect.
Well he lost the +1 magical damage and the +2 will from his character sheet. And whilst I haven't checked the +2 will the +1 magical damage wasn't working
did you try resetting the perk?