I have a 2012 BMW X3 and a Samsung Note 4 phone. I experienced the same problems with bluetooth connectivity for months starting around March of 2016. A few weeks ago I solved the problem by updating my BMW uconnect software.
After reading many threads on this issue and doing my own troubleshooting, it seems there are two explanations for all these problems: 1) the com box or 2) software incompatibilities. While it's certainly possible for the com box to fail, I believe software is more likely the cause of the majority of problems reported here. Today, software is developed using a "continuous improvement" model. This means we're all subject to a constant barrage of updates for apps and operating systems alike. When updates result in communication glitches, it generally falls to us (consumers) to discover and report the problems. This stinks because we're caught between big companies like Samsung, BMW and Google, all pointing fingers in the other direction as to cause. What a world it would be if these companies actually worked together to support their consumers.
I bought my X3 in August 2015, paired the Samsung Note 4 to it successfully and never had a problem until roughly March of 2016. Then, suddenly, I couldn't connect with messages activated and experienced the high-pitch disconnect beep in the middle of conversations. After reading various posts, I decided to perform a full factory reset on my phone. Unfortunately, this didn't resolve the issues and proved to be a fairly painful process (lost all data on my phone, even after full backup).
Next, I successfully paired my wife's iPhone 6 to my X3. No glitches, no dropouts.
Finally, I called BMW. BMW support instructed me to install a new version of the uconnect software. After restarting both my phone and the car, the major problems were resolved. It still takes minutes to sync my contacts (about 600 entries). But at least I can make reliable calls.
Because this was a software issue (for me), I fully expect this to happen again. So, lessons learned? Look at my phone update history immediately after noticing a connectivity problem. Report the problem to BMW immediately. Try connecting other phones before taking any measures on my own phone. Update all software (phone, car) to most current versions.
Threads like this were helpful, but the info presented could have been more helpful with the inclusion of phone and vehicle software versions.
Samsung Note 4: model SM-N910V
Software version: N910VVRU2BPA1
BMW Software: will update in a few days...