On what platform are you trying to play? I assume an emulator, in which case, why bother converting? What emulator are you using that doesn't have native GDI support?
Also, given that GDI is its own unique TOC format, there's no concept of "merging BINs". Not an option, as no GDI parser out there would even know where to begin with such a merge.
I've never messed around with converting GDI to CHD (haven't had the use-case), but this post seems to explain the process:
https://www.reddit.com/r/RetroArch/comm ... dreamcast/