how do I make a script that randomly makes blocks disappear and reappear?

Looking at the above script. You don't need to have scripts inside every part you can just run a single script in the same place as your path/blocks.

For instance: Tree Structure of workspace:

Workspace
|¬ Camera
|¬ Terrain
|¬ Baseplate
|¬ Obby Obstacle Path 1
    |¬ Script -- The single Brain script
    |¬ PathBits -- The group containing your Parts
Players
Lighting
<etc...>

In that Script you would paste this:

local Group = script.Parent["PathBits "]    --// The path to your blocks (Group them together in a model of folder and name the group then set the path to that group here!)
local HowmanytoChange = 256     --// How many parts to change 
local DoClear = true            --// Change Parts back to their original State on each run?
local ChanceToChange = 50       --// values between 0 and 100 are good anything beyond these might break things
local RandomWaitTime = true     --// do we have a random wait time or not?
local WaitTime = 60             --// what time to wait before each change

--//#############
--//# Main loop #
--//#############

while true do
    local Bits = Group:GetChildren() --// Grab each part in this Group
    local CBits = {}
    HMB = HowmanytoChange <= #Bits and HowmanytoChange or #Bits
    for i=1,HMB do
        local ChosenBit = Bits[math.random(1,#Bits)]
        while CBits[ChosenBit] ~= nil do
            ChosenBit = Bits[math.random(1,#Bits)]
            if(CBits[ChosenBit] == nil) then break end
        end 
        CBits[ChosenBit] = ChosenBit
    end

    for k,Part in pairs(CBits) do
        local Chance = math.floor((math.random()*100)+0.5)
        if(Chance <= ChanceToChange) then
            if(Part.Transparency ~= 1) then
                Part.Transparency = 1
                Part.CanCollide = false
            else
                Part.Transparency = 0
                Part.CanCollide = true
            end
        end
    end

    table.clear(CBits)
    CBits = {}

    if(RandomWaitTime == true) then
        wait(math.random()*WaitTime)
    else
        wait(WaitTime)
    end

    if(DoClear == true) then -- if you want to clear last change then change this value to true above!
        for k,Part in pairs(Bits) do
            Part.Transparency = 0
            Part.CanCollide = true
        end
    end
end

If you hocked everything up correctly then it should start to change when you hit run or play.

To configure the script to your liking the following values you can play with and an explanation of what they do.

local Group = script.Parent["PathBits "]    --// The path to your blocks (Group them together in a model of folder and name the group then set the path to that group here!)
local HowmanytoChange = 256     --// How many parts to change 
local DoClear = true            --// Change Parts back to their original State on each run?
local ChanceToChange = 50       --// values between 0 and 100 are good anything beyond these might break things
local RandomWaitTime = true     --// do we have a random wait time or not?
local WaitTime = 60             --// what time to wait before each change

Group = script.Parent["PathBits "] This links up the parts to the correct location

HowmanytoChange This is how many you want to change each cycle for instance if you wanted only 10 to change each time then set this to 10

DoClear Do we want to clear/reset each part back to normal before each change?

ChanceToChange How much of a chance do we want to give each part to change its state?

RandomWaitTime Do we wait a random amount of time before changing?

WaitTime The max amount of time before changing,(Note: if the above RandomWaitTime == true then this will be the max wait time for the random wait time!

If you have any Questions or have any trouble let me know and ill help! :)

Here's a long script for ya buddy, put the script in your part, not a local script, a normal script.

-- remove the --'s in the script, please don't delete the --'s after the script in the same line just like this way shown:

print(script.Name) --Print's the name of the script

--you can delete this thing above. do not delete anything below.

local part = script.Parent
--[[
local part2 = workspace.PartName
local part3 = workspace.PartName
local part4 = workspace.PartName
--]]

while true do
    wait(math.random(0, 2)) -- 0, 2 part is a random time selector, 0 is minimum, and 2 is maximum. if you don't want it to be random, the change it to be just "wait(time)"
    part.CanCollide = false -- makes the part uncollidable
    part.Transparency = 1 -- makes the part invisible
    --  part2.CanCollide = false -- makes the part uncollidable
    --  part2.Transparency = 1 -- makes the part invisible
    --  part3.CanCollide = false -- makes the part uncollidable
    --  part3.Transparency = 1 -- makes the part invisible
    --  part4.CanCollide = false -- makes the part uncollidable
    --  part4.Transparency = 1 -- makes the part invisible
    wait(math.random(0, 2)) -- the same thing as the last one.
    part.CanCollide = true -- makes the part collidable
    part.Transparency = 0 -- makes the part visible
    --  part2.CanCollide = true -- makes the part collidable
    --  part2.Transparency = 0 -- makes the part visible
    --  part3.CanCollide = true -- makes the part collidable
    --  part3.Transparency = 0 -- makes the part visible
    --  part4.CanCollide = true -- makes the part collidable
    --  part4.Transparency = 0 -- makes the part visible
end