I have upgraded to Fairphone OS 17.04.3 from Fairphone OS 1.13.0 via Fairphone OS 17.04.1 which was always mandatory as per OTA update multiple times, with and without encryption of Fairphone OS 1.13.0.
While the update to Fairphone OS 17.04.3 never failed, I had one time an issue upgrading to Fairphone OS 17.04.1. The phone rebooted with one retry in boot loader normally in Fairphone OS 1.13.0. A second time using OTA update worked out well.
I would assume it is a timing issue rather than specific to encryption setup. Would you fear to try out a second, or for @Martin_Anderseck a third time?