I think it suffices to hand the data over directly:
$("#inputhidden").select2("data", data, true);
Note that the second parameter seems to indicate that a refresh is desired.
Thanks to @Bergi for help with this.
If that doesn't automatically update you could either try calling it's updateResults method directly.
$("#inputhidden").select2("updateResults");
Or trigger it indirectly by sending a trigger to the "input.select2-input" like so:
var search = $("#inputhidden input.select2-input");
search.trigger("input");