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did the jack hole dried from water? If not sure try cleaning with clinic stix like used to clean ears or so.
When the jack hole is broken there can be seen a moisture in the camera, also you should see the screen light in the hole in dark. If not the jack is probably sealed well, but water inside can malfunction the ear phones. Try to blow with air in the jack port to see if any water will came out (can be done with mouth, or gently with a small power modelling compressor).
Considering what chemicals are in swimming pools and the warranty clearly says fresh water only then it may be possible that a reaction to the chemicals has taken place
Snap away underwater
With the waterproof Xperia Z2, you can take pictures with the best phone camera while swimming in freshwater for up to 30 minutes. You can even dive up to 1.5 metres with it. Just remember that all the covers for the micro USB port, the micro SIM slot and the memory card slot must be firmly closed.
You said and I quote "All the flaps were fully closed and I submerged it in a swimming pool for small periods of time, around 5 minutes." now your saying you didn't - You could contact Sony care http://www.sonymobile.com/global-en/support/contact-us/ or take it back to the place of purchase
As above you could contact Sony care http://www.sonymobile.com/global-en/support/contact-us/ or take it back to the place of purchase - These are your only options or try to let it dry fully before re-testing
If it's working then it probably just needed to be fully dry to make a stable connection - I'd monitor this making sure that it is fully dry before pluging head phones in