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Settings-apps-all,scroll down to smart connect. Clear data. Restart.
You should check the 3.5mm input for any dirt,scams etc.
I checked again just now. It's clean. no dust or dirt.
You can try one more thing: while you are in a call or listening to music,unplug and plug back any headset several times.
If the above does not help,you should stop by a sony service:
http://www.sonymobile.com/global-en/support/contact-us/
/t5/FAQ/How-to-get-your-Sony-Xperia-product-repaired/m-p/991374#M21
Still nothing 
I experienced some difficulties starting 2 months when plugging my headphones (all types), but they worked.
Last two weeks, i dove with the phone under water. After that, i experienced this issue. But when i did the smart connect thing (a week ago), my MDR-nc31e were detected by the phone, and worked perfectly (but not the other headphones).
But now, all of them are out.
Maybe i should take it to someone from Sony Support. It should be a hardware problem, not a soft one.
Keep us updated.