Welcome to the forum @stiobhan.
Deletion of a project directory for a CryoSPARC project that is still attached to the CryoSPARC instance leaves the CryoSPARC instance in an inconsistent state.
If you wish to delete a project directory, please delete the project first using the corresponding Delete Project GUI action.
A workaround for projects whose directory no longer exists is described in Job/project forced removal for a deleted project directory - #2 by nwong.