Apologies you’re facing this issue. This is currently a bug in Reference Based Auto Select 2D that needs to be fixed. We’ve made a note of it and thank you for reporting. Unfortunately there is no simple workaround at this time
Did you observe this issue on a job that newly created on CryoSPARC v4.7.0, as opposed to a rerun of a job that was originally created in an earlier version of CryoSPARC?