If you’re using your Lync Mobile client to make a VoIP call, and a cell call comes in, your Lync call is put on hold. This isn’t so much an issue with Mobility or the Lync client as it is with the design of your phone. A smartphone with a poor cellular calling experience is bad news, so when a cellular call comes in it is given priority over all apps. There’s not much an app designer can do about this. Your best bet when taking Lync calls if you want to avoid this issue is to only make calls via the cellular network. This isn’t a great workaround, however it’s better than unexpectedly having a conference call paused. To enable this, go into the options section of Lync mobile and set Require WI-FI for voice to on. When you make, answer or join a call from Lync make sure you’re not connected to WI-FI. Lync will call your mobile device using your mobile carrier and connect the call this way. An incoming cell call won’t put an existing cell call on hold and your conference or VoIP call will continue uninterrupted. Of course, this workaround only works if you have Enterprise Voice enabled to make an outbound call.
Your other option is to simply enable Do Not Disturb (for iPhone: http://support.apple.com/kb/HT5463) on your device to avoid incoming calls during your conference. This may be easier, but you might miss an equally important call.
As you may have guessed, this isn’t just a Lync issue, it will be an issue with all VoIP applications as long as your phone is accepting incoming cellular calls.