On my High Sierra system with XCode 10 I get warnings about outdated .tbd files like
ld: warning: text-based stub file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd and library file /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib are out of sync. Falling back to library file for linking.
whenn running c++ from the command line. So I dived into it and found the 'tapi' utility to create .tbd files from header files or dylibs. It is hidden deeply in Xcode, the path may be different in other versions, but running it like
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/tapi stubify libGL.dylib
did the trick for me, generating new stub files with current uuids. You possibly need to disable the system integrity protection (see Operation Not Permitted when on root - El Capitan (rootless disabled)) to put them in the system area then, though.