Tool Is Gone ?

Two problems. You need to use :Destroy() rather than :remove(); remove() takes up extra memory as it doesn't actually delete them from the game, just sets the parent to nil.

Also, you need to create a new clone each time. Your problem was that :remove() was setting all of the descendants' parents to nil, so when you set the clone's (the one that you only cloned once) parent, all of the children were gone.

To fix this, all you have to do is move cl2 to under the if statement, and use :Destroy() instead.

local cl = game:ReplicatedStorage:WaitForChild('WoodenAxe')

script.Parent.MouseButton1Click:connect(function()
	if Bought.Value == true and Equiped == false and AnyEquiped.Value == false  then
		local cl2 =  cl:Clone()
		print('All Requirements Met')
		Type.Image = script.Parent.Parent.ImageLabel.Image
		cl2.Parent = player.Backpack    
		script.Parent.BackgroundColor3 = EquipColor2
		AnyEquiped.Value = true 
		Equiped = true
		script.Parent.Text = 'UnEquip'
		sound:Play()

	elseif Bought.Value == true and Equiped == true then
		Humanoid:UnequipTools()
		wait(.1)
		Type.Image = NA.Value
		if player.Backpack:FindFirstChild("WoodenAxe") then
			player.Backpack:FindFirstChild("WoodenAxe"):Destroy() --// findFirstChild is deprecated, use FindFirstChild instead.
		end
		script.Parent.BackgroundColor3 = UnequipedColor2
		AnyEquiped.Value = false
		Equiped = false
		script.Parent.Text = 'Equip'
		sound:Play()
	end
end)

Hope this helped.