Thanks again for your help!
I tried the swapon/swapoff solution you proposed. Unfortunately mkswap is fixed now and always add UUID. The closer I got was to create an ext3 replacing the swap. Then I cleared the UUID of the ext3. There is no way though to convert this into swap keeping the empty UUID.
I thought of a solution but it requires changes to flopswap. As you know the internal swap doesn't have a label while swaps at SD are labeled sdswap1 and sdswap2. If I changed the label of internal swap to e.g. "swap" flopswap could also check for internal swap using this preagreed label.