I wish I could find the old article on system center central, about discovery not working and the reg hacks they had to perform in order for the discovery to work.
We deployed the Lync 2010 MP to SCOM 2007 R2 a few years ago. I told the Lync Admin that he needed to do some things in order for discovery to work. He did these things, and yet we were still not getting any discovered inventory.
I googled, and found an article on System Center Central about a similar problem. We designated one of the lync servers as a discovery agent (per the advice in the MP), however our discovery data was TOO large for an agent to process (over 5 MB maybe?).
There was/is a hard limit for agents, management server, I believe is like 15 MB. So according to the article on SCC, (the person worked with PSS on this issue), they had to add a reg key to a management server which would make it a discovery node
for Lync. Then I think you had to add it to the lync pool, maybe not, I forget, but you might have to manually add it to a Lync group. Once we did this, our large Lync environment was discovered and is monitored to this day.
We are moving to SCOM 2012 R2 soon, so I will have to find out what I did (since I failed to document it), so as to replicate it for SCOM 2012. I believe this agent discovery ability may not have been fixed in 2012, but I could be wrong.
Anyway, first thing to do is send the MP guide to your Lync admin and have him/her read through it and configure lync accordingly. If after that nothing is coming in, then you can turn on logging on one of the discovery Lync nodes, and you will probably
find that it's hitting it's discovery buffer limit and dropping it all (as we did). Then you will just have to hack the reg on one of your management servers, and let it be the discovery node. Our environment has not been negatively impacted by
this additional workload, but get guidance from your MSFT resource before doing so...if this is your issue.
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