As of 2013-10-02, the redirects for issues and pull requests in the old Bootstrap repository appear to be functioning, so no edits are necessary.
Generally, there's supposed to be a redirect from the old GitHub repository to the new one in cases like this. This wasn't working after Bootstrap's transition to its new organisation, so someone opened a relevant issue.
Since it was marked closed, I assume that they got things sorted out at the time, but as it's broken now I've gone ahead and asked if the current behaviour is expected. If it isn't and the redirect can be (re)fixed, then there's no need to edit anything as the links should just start working again once the problem is resolved.
If, on the other hand, nothing can be done, the best course of action is likely just to edit them as you come across them. The last time something like this happened, it looks like the community was able to band together to get the job done, so an organised effort might be worthwhile if you were hoping to get it done sooner.
Unfortunately Data Explorer's current hardware appears to be insufficient for querying for the old URL against all of the post bodies on Stack Overflow, otherwise we could get a better feel for the scope of the issue. You can always just do a site search for the URL now that URL wildcards are supported, which I suppose makes more sense anyway.