OK so man was I stupid
 

Every time I did a mod, I only updated a single style on my board. Is there any way to force the changes so they are applied to all styles?

Have one style which is a parent of all the others, this way the children inherit the changes made to the parent.

And then go through all of the child styles and revert the templates that are red. That way you can just change the one style from now on. :)

What if the styles are totally different? You can just make any style the child of another?

Yes, if you have two different styles, but want to make alternate versions of each, you can make more child styles under both. Then you can make child styles under those child styles too, etc.

Oh man, NOW you tell me.

I have been manually editing vBulletin Default and a third-party skin all this time. Some of the templates are wildly different though, so I imagine I'd still have to be going in and editing both...?

Yes.

Thanks gang!!!!

Another quick question - if/when I upgrade vbulletin, will it wipe out all of my template edits?

No, it will make you go through and update the ones you changed but you can do it manually.