We are running Lync Server 2013 and using the Lync client in several conference rooms at our company as well as using it on local workstations. Occasionally during a Lync meeting our users will either dial out to phone number or have someone dialing in to an active meeting and upon call connection find that the "merge call" option is missing from the ellipsis menu. Has anyone every experienced this? Is this a but in the Lync client or a configuration issue?

Once the call to be merged has more than one participant, it will disappear from that menu. Is that possibly the issue?  If not, what other options do you see on that menu when merge is missing?

Hi,

Did the issue happen only for you or for multiple users?

If the issue only happen for one user please try to delete Lync user profile and then test the issue again.

%UserProfile%\AppData\Local\Microsoft\Office\15.0\Lync

Please also make sure Lync client update to the latest version.

Best Regards,
Eason Huang

The issue is sporadic. Sometimes merging works and sometimes it doesn't. We are using the Lync SDK to automate some things in these rooms but even when the merge issue happens using just the Lync client alone does not work for call merging. Also the issue is not occuring in "all" rooms and happening consistently so I am doubtful that it is related to our custom Lync SDK code. 

What do you mean rooms?  Do you mean a conference with multiple participants?