Ok, nice model and very well organized, so it was not hopeless !
I edited the red base group , made some guidelines to remember the center of the holes and just deleted the geometry which represented the holes. Faces healed themselves. I then made a cutting component (Pink) and placed them on the original holes. When creating the component I placed the origin in the center of the top circle. Thus making it easy to place them from the component tray ( then edited the component by pulling the top circle 1MM up, so those top-faces wouldn’t interfere with the top-face of the red base-group.
As you see, I am using the copy of the cutting component to edit: I am not scaling the component itself, I am editing the component (double-click) and selecting all of it’s geometry. Then scale it to desired dimensions. This scaling can be controlled by center (Option on Mac, Ctrl for Windows) and adjusted by exact measurements by typing the desired measurements ( e.g. 22mm;22mm) You must use the units, otherwise it will use the relative scaling factor! When the holes are your liking, apply the solid trim or intersecting tools.