I'm not completely clear on what you want to say, but let's assume it's something like:
When you have a twin sister, you often feel like you can read each other's thoughts.
You are correct that this means you are one of the twins. If instead you want to distinguish them as separate people, why not keep it simple:
Twin sisters often feel as if they can read each other's thoughts.
If you want to maintain that sentence structure, "When you have ..." you might have to add more information:
When you have the situation where there are twin sisters, they often say they can read each other's thoughts.
This is somewhat verbose, but clear. However you may be able to shorten it:
With twin sisters, they say they can read each other's thoughts.
Naturally you may have to adjust this if you want to say something different. In any case, the use of the third-person "they" clearly indicates you are not one of the twins.