You could try the TWRP way …
Attention! This will remove the installed OS and all your data from the phone (which the “factory reset” available in the OS will not completely do by the way, so don’t bother with that).
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Put a microSD card into the phone.
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Get TWRP running as recovery:
Download a TWRP image already adapted to the slightly changed hardware of the new Fairphone 2 batch here, currently TWRP_3.1.1-0-ota-fix.img.
To install this image, follow the “Fastboot Install Method (No Root Required)” section given here, mind the image filename (they give a different one in the instructions). -
Put the right OTA file on the microSD card, currently fp2-sibon-17.08.1-ota-userdebug.zip, not one of the switcher files.
If you want, you could combine this with the next step: -
Boot the phone into TWRP.
If you connect your phone to your computer now, you could transfer files.
In TWRP:
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Settings - uncheck “Zip signature verification” - back to main menu
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Mount - check “System”, “Cache”, “Data” and “Micro SDCard” - back to main menu
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Wipe - Advanced Wipe - check “Dalvik / ART Cache”, “System”, “Cache”, “Data” and “Internal Storage”, do not check “Micro SDCard” - Swipe to Wipe - back to main menu (if it doesn’t return automatically)
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Install - Select Storage: “Micro SDCard” - select the OTA file from the list - Swipe to confirm Flash - when finished, reboot (this reboot really might take a while, so be patient)