Or actually you can right click on the retacgular pattern, then go to object/explode.

This step will help break down all the holes pattern into separate hole feature. Then only you go to delete those unneccesarry hole features.

But bare in mind that, this is only one way feature. Is no way to combine them into one pattern feature. If you really wan to keep the design change reflect to first hole. THen you should choose user defined pattern as what mention previous replied post.

THanks.