Yes I have checked in my changes also tried logging out and relogging.
there is no UI th case is always started with Add. so after deletion, saving i rerun the case and then this issue occurs.
To reproduce the scenario below are the steps.
Have a Case with 2 stages and each stage say have 3 steps.And in first stage 3rd step have pre-condition so that it will never enter and always skips, make sure first 2 steps have some utility not assignments.
After that delete the 2ns step and run the case then the case terminates in first stage without going to 2nd stage. you introduce that 2nd step again then run again case goes to 2nd stage after completion of first stage.