Hi,
Try using the earphones with the microphone attachment.
If you can be heard all the time this proves that the voice transmission circuitry is OK but that there is a problem with the phone's microphone. It is either intermittently faulty itself or it has a loose connection to the systemboard.
Here is a link to the Ifixit guide on how to replace the microphone in your phone.
Fairphone 2 Microphone Module Replacement
If you still experience the problem when using the earphones with the microphone attachment then there is a problem with the voice transmission circuitry in the systemboard.
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