The problem now, you to your own making, is that you may have to replace the entire unit. That stuff really sets up, but never make the water tight seal it promises. You will have to cut out the damaged piece and replace it.
The top shell of the water heater is the most important part of the heater next to the gas control valve, T&P valve, tank, and the remaining outer shell less insulation.
Just last week I ran into a similar situation where someone tried to repair something, well let me tell you...I'm glad to be alive!

It will bust right off.