I think the answer lies in one of the SO posts linked to in your question:
I made a sample project to reproduce this issue — and found that it
would only occur when the app receives a SIGKILL signal, like when the
debugger is stopped from within Xcode. In my experiments, unhandled
exceptions, crashes, exit() and abort() don’t cause
NSHTPPCookieStorage to loose data.As this looks like a debugging-only issue (it only occurs when using
the debugger), I closed the radar I filled previously.
You can test this by restarting the phone normally and observing that all changes to NSHTTPCookieStorage are correctly persisted and reloaded.