Well, just to add my experience - quite the same as previously stated.
We have two FP2, both FPOpen and “rooted”, one with XPosed/XPrivacy one without.
When the Updater showed up “new version available” I did not imagine it would be the long awaited upgrade to Android 6 - so I did not take any precautions (backup apps / nandroid-backup).
Both phones were in a boot loop after the OTA-update. Sometimes I managed to enter the PINs, most of the time the phones did not accept any input.
Finally I decided to down- and upgrade the FPOpen as described further up. In Detail:
- downloaded
fp2-sibon-17.04.0-manual-userdebug.zip(Link somewhere up in this forum) - downloaded
fp2-sibon-17.06.4-ota-userdebug.zip(from https://code.fairphone.com/) - unzipped the
...17.04.0...zip - started the FP2 in Fastboot-Mode (Power-On + Vol-Down)
- run the
./flash.shin the unzipped folder - rebooted phone (Android 5.1, stuck in boot-loop, optimizing apps)
- switched off by pulling out the battery
- booted into Recovery (Power-On + Vol-Up)
- in TWRP went to Advanced -> Sideload, on PC did
adb sideload ...17.06.04...zip - rebooted
- phone started normal with Android 6.0.1
My system settings were all there (including photos, SMS, contacs, call-log), but all application settings (including data) were gone.
I managed to recover the most important settings from old Titanium Backups and a nandroid-backup (I made after the first upgrade in TWRP).
The recovery of the two phones took me about 10 hrs. 
I really appreciate the work the Fairphone-Team is doing, but an major upgrade has to be announced in some way - this one showed up like any other upgrade before.
And on top it seems like the bug was well-known before - this is not professional work. 