Penalty of removing facility

When you fail to save enough civvies, you lose contact with the resistance in that area, and will have to reestablish contact by scanning the area again. While contact is lost, your radio tower in the area will not be available. Even after contact is reestablished, you suffer a penalty to the amount of supplies they provide per month.

Yeah, I started the game 4 times until now and every time it was completely random...

My current game is on Legend and my HQ is in East Asia. I have 2 Avatar facilities, one in West Asia, one in Australia.

Also keep in mind that various missions or hacking towers can lead to discovering more facilities.

I understand your frustrations but try not to worry too much about the avatar project completion. Instead, always try to ride the clock.

What I usually do, I wait until the avatar project is almost done, this including the final countdown. In the mean time I try to be as prepared as possible and enable 1 or 2 facility missions. After the countdown is close to an end I do a facility mission, making the avatar project to reset the clock and go down 2 squares. Then I wait again for countdown, do another mission and so on. That boost in the beginning is very important. Without it, playing on Legend is almost impossible... so take your time!