Someone at Soul Society would definitely know what was going on. Or, at the very least, Yui knew. Otherwise, she wouldn't have sent him that message.
The issue about going to Soul Society… more accurately, the Soul Society base that Natsuya knew about was whether or not they could obtain the information they wanted there.
While rescuing his companions, Seiji hadn't seen a single conscious person anywhere. Due to the pressure of the giant mystical red cherry blossom tree, even ordinary spiritual ability users and Awakened had fallen unconscious. What was Soul Society's base currently like? Were there people that had managed to remain awake there? And if so, would those people know anything? All of this was unknown.
Although the result of going there was uncertain, Seiji agreed that this was probably the best option to go visit first.
Right as Seiji made up his mind to go visit Soul Society, he suddenly heard a voice...
"Help me…"