GetChildren function not working?

The problem here is that the GetChildren function returns a read-only TABLE of the function. You cannot do script.Parent.Parent.Close:GetChildren().Transparency = 1 because it's not that simple. You have to use a for loop to go through each child in Close and perform the action as such.

local Open = false
local Joe = script.Parent.Parent.Close:GetChildren()
local Bob = script.Parent.Parent.Open:GetChildren()

function Click ()
	if Open == false then
		for _, child in pairs(Joe) do --I assume you are familiar with generic for loops
 		       if child.Name == "Part" then --Capitalize Name, it is the name of a property
				child.Transparency = 1
				child.CanCollide = false
			elseif child.Name == "Window" then --Use elseif instead of multiple if statements
				child.Transparency = 1
	            		child.CanCollide = false
			end
		for _, child in pairs(Bob) do
			if child.Name == "Part" then
				child.Transparency = 0
				child.CanCollide = true
			elseif child.Name == "Window" then
				window.Transparency = 0.5
				window.CanCollide = true
		end
	Open = true
	elseif Open == true then
	        --You get the point by now
	end
end

script.Parent.ClickDetector.MouseClick:connect (Click)

If you are not familiar with generic for loops, check out this article on the Roblox Wiki for help. If you had any problems understanding these concepts, just ask me and I'll edit my response. I hope my answer was helpful! You can upvote and accept it if you thought so.