Maybe before this life started the two souls, having shared many a fulfilling life on Earth in the past -- and anticipating many more to come -- have decided to do other things this lifetime. Maybe each is perfectly content because this was a mutual decision, and one is anyway able to reach out and "touch" the other in a spiritual sense whenever desired. Maybe ...
You're right @yawnguy, although in my opinion these souls once they meet, they shouldn't separate, but ... it's life.
My view is that this is a l-o-n-g term arrangement, many lifetimes. Any such temporary separation would be done by mutual agreement, maybe for spiritual growth, maybe for some greater good where an intimate relationship with another would get in the way. This is different to a short-term human dating relationship -- far more familiar to us all! -- where one of the pair wants to move on but the other wants to continue.