by different looking chip you mean different layout of components on the board, right?
You likely had a reference design one and the new one isn't reference design. (or the other way around or neither were reference design).
If you give me the model number of the gpu and the water block you're using, i can tell if they're compatible. Or you can just try it. Just make sure all the parts that need to be cooled are making contact with the block. (gpu, ram modules, voltage regulators, maybe other things depending on the waterblock)