Hmmm, I've tried that, and here's what happens exactly:
* Go to the guild progress page
* Both of my guilds are listed, and both have the instance selection dropdown and a submit button, my primary guild is listed first
* Both dropdowns initially show "Naxxramas: 10 man" in their respective dropdowns
* I select "Obsidian Sanctum: 10 man" for my primary guild in the first dopdown and click Submit
* The dropdown resets to "Naxxramas: 10 man" for the guild I want to update and only shows Naxx achievements
If I repeat the above but instead select "Obsidian Sanctum: 10 man" in the second dropdown, i.e. the guild I do NOT want to update, then OS achievements show up, but I don't want to update them for that guild, only the first guild.
Thanks in advance!