Do you mean "Skype for Business" aka Lync? Cause that's really totally unrelated to Skype except for questionable branding. Skype used a heavily obfuscated system, with all sorts of anti-reversing technology.

And the protocol flowchart for Lync is complicated as all hell, even with SIP at the core. (More complicated than SIP usually is.)

I wonder if Skype itself falls under MS's legal obligations to publish protocol descriptions.