I can reproduce the same problem on my project.
The errors have nothing to do with Debug Symbols. These messages in the output are the key:
file was built for archive which is not the architecture being linked (arm64):
/Users/Shared/UnrealEngine/4.13/Engine/Binaries/IOS/UE4-Engine.a
I have checked that all “.a” files (static libs) pre-built for IOS are only built for 32-bit architecture. However, Shipping libs (e.g. UE4-Engine-IOS-Shipping.a) are built for both 32-bit and 64-bit architectures. This is the output of file utility for Shipping libs:
UE4-Engine-IOS-Shipping.a: Mach-O universal binary with 2 architectures
UE4-Engine-IOS-Shipping.a (for architecture armv7): current ar archive random library
UE4-Engine-IOS-Shipping.a (for architecture arm64): current ar archive random library