Combine source maps of two compilation steps
Try sorcery - it's designed for exactly this purpose (I'm the author, I came here looking for info on related tools). As long as the .map files are in the correct location (or inlined as data URIs), you just run sorcery on the generated file and it will locate the intermediate sourcemaps and compose them.
As best I can tell from the source map specification (and other discussions), multilevel mapping has not yet been defined
Source Maps Revision 3;Multi-level Mapping Notes
Someone may have developed some tools to address this, maybe in a Github repository. Of course you have both the tools to generate such maps, and browsers that can use them.
https://hacks.mozilla.org/2013/05/compiling-to-javascript-and-debugging-with-source-maps/https://github.com/fitzgen/source-map
Closure Compiler now implements --apply_input_source_maps (and --parse_inline_source_maps to boot). That should do exactly what you're trying to achieve here, no additional tooling required.