I am assuming you are talking about recessed lights? Have you talked with your electrician? It's usually not a problem to add/move/delete lights, it just costs. However, if you plan to remove some then you'll need to fill holes and repaint. Are the lights the same colour as your ceiling? If they are the same colour (ie. white on a white ceiling) then they don't stand out as much.

It's not hard, any good builder should be able make good the ceiling. It's unfortunate to have to pay twice for something. How far apart are the lights? Are they LED's or Halogen?

I understand how you feel, as I have been in some homes and it looks like a runway on their ceiling. What I worry about, is if you remove every other one, then you may be left with too little lighting in the room or inconsistent lighting (light and dark areas).

It can be a bit tricky judging by a picture, but maybe consider removing the row along the wall, it looks like they are very close. Usually, you use recessed lights for general lighting. And other lights for purpose lighting, such as a floor lamp for reading, under cabinet lights for prep work and pendent lights over an island.

Your electrician will provide you with any certificates if they are needed (just ask). As you can see in the picture below, we sparingly put in recessed lighting (halogen) at 4 feet apart and they light the room beautifully. We also put in under cabinet lighting for prep work, however, rarely get used.

BTW I love the pendant lights, where did you find them?

You're renovation looks fabulous. Though I fully understand how you feel about the spotlights. I have a similar concern with the extension that we are doing on our house at the moment.

How about adding a normal chandelier in your living area?

Do you have any scope to add some of the spotlights onto another switch? i.e. one switch switches all of the lights on an another switch maybe only half of them?

If you don't mind me asking which sliding door company did you go for in the end? we are just finalising ours and its a toss up between; ID Systems, Raeyners and Dutemann.

I hope you work it out with minimal cost.