El-Aurians have something similar to an eidetic memory. They are widely known for being able to recall with absolute clarity something that happened hundreds of years ago. It's possible that this ability allowed Guinan to perceive the differences in the timeline during "Yesterday's Enterprise", but there's an alternate explanation as well.
An unused scene in the ST:G script explained that the El-Aurians who had been trapped in the Nexus - including Guinan and Soran - had a unique perception of time afterwards. This is also alluded to in the TNG novel "The Buried Age."
The TV episode was filmed far in advance of the movie, however, so at that point the writers had no idea that Guinan was ever trapped in the Nexus, or even that the Nexus ribbon existed. There's no explanation given within the episode itself, but this is the closest we have:
GEORDI: How could Guinan know that history has been altered... if she's been altered along with the rest of us?
DATA: Perhaps her species has a perception that goes beyond linear time.
Then, later we get this statement from Guinan herself:
GUINAN: I don't have alternate biographies of the crew, Tasha. I told the captain... it's just a feeling.
So, without hearing from the writers themselves, we are left to assume that the original intent was for El-Aurians to have a "sixth sense" that made this possible. This was later going to be retconned so that only the El-Aurians trapped in the Nexus had this ability, due to their Nexus exposure. Since that scene was not included in the final movie, it probably isn't considered canon, however.
To answer your original question, all of this leads us to believe that - regardless of which circumstance or ability allowed Guinan to "feel" the difference - this ability would only extend to the individual El-Aurian's specific universe/dimension/timeline. So, essentially, each "version" of Guinan would feel that her own version was the correct one, and she would only sense changes done to THAT version.