It's not about deleting obstacles from a level, it's about removing an entire
obstacle (ID) from the game how it seems.

I already did a small test in form of a bisect as explained in the message above.

before b288109dcbf7d6fb245175c35392d852006d0a4b, everything was fine
in b288109dcbf7d6fb245175c35392d852006d0a4b we removed one obstacle
after b288109dcbf7d6fb245175c35392d852006d0a4b we had the sign messages shifted
by one
then I did a1c0e65b670b0fc731b1076d84c71f01e9a07d18 which caused the sign
messages to be shifted by two, its still this way now.