In season 3, a short dialog between Harry and Barry (Harry notices the changes to the timeline because he just came from another universe, that was not affected) establishes that changes to a timeline only affect one universe, so every universe has its own timeline.
On a first glance that sounds logical. But on a second (fridge logic) it does not. If the timeline of Barry's universe is changed, than all events of interaction with the other universe are changed, too. For example in the Flashpoint timeline, I assume Berry never traveled to the other universe (it was "the other" Flash I assume?) And even if the timeline is changed slightly so that he travels over there a bit earlier or later or with another hair cut, the timeline of the other universe has to change, too.
Only in the case the timeline is changed completely, so that he never travels there, the "time remnant" mechanism could kick in and a time remnant Barry will visit the other universe out of nowhere. But what about visitors of the other universe? How can they (in the new timeline) still visit the old timeline? In the Flashpoint timeline doesn't zoom appear? Doesn't Harry and his daughter visit our universe? If yes, how can they, on a later timeline, visit and remember the old timeline? Or in the slightly altered resulting timeline, how can they not remember the speed laboratory? They must have seen it on their visit in this altered timeline.
Is this a plot hole or is it explained somewhere in or out of universe?