Unfortunately, you should expect a refusal.
My previous application was rejected for the exact reason. My WES Summary only had bachelor's degree but did not include the diploma. However, the individual analysis had evaluated both B.Sc and PG Diploma to Canadian equivalency.
I took a back up IQAS ECA which included both B.Sc and Diploma in Summary and sent that through CSE explaining the WES mistake. But I was still refused stating I did not submit IQAS ECA at the time of submission and therefore it cannot be considered to evaluate my education.
I consulted with an immigration lawyer and he advised me not to appeal because the decision will not change since it is not a mistake from IRCC. As long as WES Summary shows only one credential the decision will remain same. It is better to reapply with IQAS ECA.
I would strongly advise you to withdraw your application and try getting ECA from IQAS or ICES. These two organizations will definitely evaluate you with 2 degrees in the summary.
Please how do you know your VO?