I evaluated on my Masters and used the ECA provided. In your case, you should have used just CES because that’s your highest qualificationBuddy, let me tell you my scenario clear:
I sent my Bachelors to WES in the year 2019 and WES gave the Bachelors equivalency
I then completed my Masters one year later -> Initially sent my Masters to WES -> WES has also asked my bachelors along with Masters for an updated report -> Gave them both -> WES outcome is 4 years Bachelor's and 1 year PG Diploma.
Was not satisfied with this. Sent my Masters alone to CES -> They evaluated as Masters -> Got Master Equivalency
I then updated my profile as Bachelors from WES (although the WES report has a Bachelor equivalency and Master degree as PG Diploma) in one row.
In the next row (under the education row of EE profile), I added my Master's report and updated the CES reference number there.
After the ITA I submitted the ECA report of WES (for Bachelor's) and CES report (for Masters). While receiving the ITA, my profile had bachelors and masters and hence had to provide to them both. Cannot skip one of them, as I got ITA with this info.
Now if the Visa officer reviews my bachelor's ECA, he will open the WES report and find bachelor there. When he reviews my masters, he will find the CES ECA there. My worry is while looking at my bachelor ECA, if he finds that PG diploma for Masters is awarded by WES and for the same degree, CES gave masters, will it not create issues?
I have very clearly denoted in the application that WES is only for bachelors and CES for masters.
I hope all goes fine, cos this is not only for me. Many would have crossed this hurdle (especially from India) and gotten the PRs I suppose.