How to encode mkv that already has AAC audio?

[StriatedFoot]

I have some mkv files that are avc with AAC audio, and I'm wondering if it's possible to skip the encoding audio stage?  XenonMKV converts the AAC to wav and back to AAC again, which I'd like to avoid.  So far, it seems my only alternative is to mux the XenonMKV'd video file with the original audio file manually, which is a pain because I have about 50 files to do.

PS - I *think* the AAC files are AAC-LC, but I can't be sure.