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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.
Instead of exploding your pattern as suggested, use Catia's ability to deselect the holes in the complete pattern that you don't require.
When you are defining the pattern Catia shows in its preview each of the patterned objects i.e. in your case each new hole. For those that you do not require simply click the orange dot associated with that hole. This deselects the hole but leaves the pattern as a pattern that can be subsequently reworked or modified as required. If you require it later you can reclick the dot and it will be integrated back into the whole pattern.