How do I make this script reset itself every few minutes?

Just put it in a loop that only runs every so often

--First of all you will need a way to reset the rooms that were already in place
local rooms = Instance.new("Folder") -- Create new folder to store the rooms in
rooms.Name = "Rooms"
rooms.Parent = workspace
local timer = 60 -- Change 60 to however many seconds you want to wait inbetween room changes
while true do
	rooms:ClearAllChildren() -- Removes all previous rooms
	local rooms = game.ReplicatedStorage:WaitForChild("GeneratedRooms"):GetChildren()

	for I, placeHolder in pairs (game.Workspace.PlaceHolders:GetChildren()) do
		local chosenRoom = rooms[math.random(1,#rooms)]:Clone() -- You had it set to #room? I think you meant to have it as #rooms. That just says to choose an index between 1, and the number of items in the table. 
		chosenRoom.PrimaryPart = chosenRoom.Floor
		chosenRoom:SetPrimaryPartCFrame(placeHolder.CFrame)

		placeHolder:Destory() -- Not sure about this, if you destroy the place holders you wont have any to set the next rooms at. But I have no idea what you have going on as placeholders, if they are just invisible parts just set them to cancollide false so you can keep using them
		chosenRoom.Parent = rooms
	end
	wait(timer)
end

-- You may also want to move the player so he doesnt fall to his death when old rooms are destroyed, in that case just use character.HumanoidRootPart.CFrame = SpawnPart.CFrame * CFrame.new(0,3,0) before you :ClearAllChildren()