Deletion of files managed by CryoSPARC by non-CryoSPARC means, such as by the rm command, will disrupt CryoSPARC. CryoSPARC project data that are no longer needed and wanted should be deleted via the CryoSPARC interface so that CryoSPARC can track the deletion.
In case the deletion of CryoSPARC-managed files outside CryoSPARC has occurred, you may try the suggestion in Illegal job id "submitted." when trying to get status - #6 by nwong.