Yeah, you are getting a bit into the weeds, but the common code thread definitely has the answer for you adding to an trait die. Although, the common method is to use that for a skill rather than an attribute and no attribute will ever be below d4. In essence the effect of the archetype is to add +1 die type to Vigor UNLESS Vigor is already d6 or higher, correct? In that instance you would just have to enclose your +1 die type in an if statement, is all. You just need to make sure you get the timing right. It will probably need to be early, so I'm guessing something like Pre-Traints 3000? I'd have to play to figure that one out.
Removing that bonus... first off to characters change archetypes all the time in that game or something? If not, then no problem, if they do then I would think that if you changed the archetype that code would go away and that code would only apply itself while that archetype were active. If it's pulled it should pull the extra die with it... maybe. I mean once you advance a boosted Vigor it would no longer be a d4 at the base... Hmm... that almost makes it more like a Super Attribute in effect, which would be something activateable. I couldn't really tell you off the top of my head, though, i think I'd have to play around to really figure that out.
I would only add one more comment, though, which is that it's sometimes fine to just not automate everything through HL. Sometimes you just make a note in your descriptions to tell the player to do the thing they need to do.