Just setting Skip Install to YES did not work for me. Hopefully this will help somebody.
I went to dependence of my project targets: Coreplot-CocoaTouch. Then went to Coreplot-CocoaTouch Targets. In its Targets opened Build Phases. Then opened Copy Headers. There I had some of headers in Public, some in Private and some in Project. Moved ALL of them to Project.
Of course, in Build Settings of Coreplot-CocoaTouch Targets checked that Skip Install was set to YES in Deployment options.
And this time Archive made an archive that could be signed and .ipa produced.