@sjlombardo Ah sorry, I forgot to edit my last reply.
I’ve fixed the problem, it was again the fact that -framework SQLCipher wasn’t first up in the list (as you’ve said in your iOS 10 * Xcode 8 post).
For the sake of others who might have the same problem; please check the CocoaPods-generated xcconfig files. It seems that, even though you specify SQLCipher as the first pod, it won’t be the first flag in the OTHER_LD_FLAGS setting of the generated xcconfig file. This is especially the case if you use multiple schemes (as I do).
And again, please don’t go through the same headache-loops as me; be sure to double check the generated xcconfig files!
@sjlombardo, thanks for taking the time to help me every time.