The EA help guy I talked to claimed it was server issues.
Apart from losing characters, buildings disappearing when I place items (not just tracks, other SH decorations too), I've found the game also keeps resetting characters already set on tasks, so I find them wandering aimlessly around Springfield.
I am too afraid to bring Lisa out from inventory, cuz the last time I did it she disappeared again. And there's almost no point on sending the buggy characters to do Rail Yard tasks because they keep resetting. I'm hoping all this will go away once they update for the end of the Monorail event.