[BirdOPrey5]

Although kh99's plugin will work just fine I'll still answer the question in case someone else searches for this and needs the info...

Mod's that change the look/layout of the forum by adding new links, new graphics, pieces of text, whatever work in 2 possible ways.

One option is they ask you to do a manual template change- in this case simply not doing the manual template change to your Theme B will keep the mod from showing in Theme B.

But other mods automatically make these changes using the Template "Hooks" system. A hook is a line of code in a template that vBulletin can inset extra code into if a plugin tells it to do so... There are many hooks available, I think in the hundreds maybe. So first figure out what template is being altered by the mod... for example lets say the mod adds a new link to the "Community" drop down menu on the navbar. In this case open the navbar template and search for "hook" - in mine there are 9 hooks... one of them is $template_hook[navbar_community_menu_start] - if the new link is at the top of the menu then delete this line of code. If the link is at the end of the menu then you'd delete the next hook, $template_hook[navbar_community_menu_end].

It should be fairly easy for an experienced user to tell what template is being modified but if you aren't sure you could look at the plugin code for the mod and look for the name of the template hook's used in the code and then find and delete them.