New characters like Kurohime who you get during the time skip are removed when you leave the time skip area, as they aren't supposed to be available for your party in the first part of the game.
Maybe having only new characters in the party caused some problem. I'll take a look at it.
You should be able to get your party members back at most locations where the party is split and later re-joins. For example the bathhouse in Aldlyn is usually a place that works to bring back "lost" party members.