I don’t use Dual-SIM, so I have no experience with that. Some generic thoughts …
Try to put the second SIM into the phone again, perhaps this reseating already does the trick (seems to work for all kinds of cards now and then with a little luck)?
Try to swap the slots for the SIM cards.
If the fault lies with some malfunction of the OS, a factory reset might not fix this. A factory reset on the Fairphone 2 only deletes all Apps and user data, leaving the OS as is (it doesn’t get re-installed or anything).
Instead …