I think you are misunderstanding how visas and duration of stay work. You having a B1 visa doesn't mean "you cannot be in the United States after 6 months after you first enter the U.S. on this visa", but rather, "on each entry to the U.S. on this visa, you can be given up to 6 months of stay".
How much you are given exactly is up to the whim of the immigration officer when you enter. Even on your first entry, the officer could give you just 1 month of stay if he/she felt like it. Conversely, even if you stay for several months, leave, and soon re-enter the U.S. on that visa, the officer could still give you 6 months of stay. It all depends. There is a tendency that if you've spent a lot of time in the U.S. already in the last year, that they will not give you the full 6 months, since you are not supposed to be residing in the U.S. However, there is no hard and fast rule.
If you are just transferring, which will take 1 day, I don't think it will affect the duration of stay on your future entries.