In some of my projects I've split things into separate link steps, which is what I'd assumed you were doing. That would require a multiple .dbg mapping.
To handle both styles, it could be a list of entries with 3 pieces of information?
- 1. .dgb file
- 2. MEMORY block
- 3. ROM location override (presumably just the start address?)
I suppose as an alternative workaround, though you could process the .dbg file to inject the final ROM addresses back into it. (Or in my case, I could synthesize a .dbg file of my own from the separate ones.) From FCEUX I was already used to having my own script to build the .NL debug files anyway.