If the encryption itself is the problem @StephanK is right. You can use the latest TWRP and it will ask for your encryption password when booting into it.
Initially there was no official TWRP for the fairphone and especially non with support for encrypted devices. (also discussed in this topic: ✏ Porting TWRP recovery in the meanwhile it has become a wiki post)
Link to the community port (or more exact it is an official one now) can be found here:
https://twrp.me/devices/fairphone2.html (Europe download: https://eu.dl.twrp.me/fp2/)
I was able to decrypt, backup (be aware /data/media is excluded) and flash new roms with TWRP 3.1.0-0.
What I was not able to do up to now is, to mount a USB-OTG device to write my backup to it. (in the past, with an Nexus 5 and TWRP I was able to do so)