I'm still really interested in concrete specifics of what has been lost. Right now it just sounds like magic, which leaves me skeptical. I'm a huge fan of programming languages as a field and hope to someday do research in it, and this is a bit of history I'm not well versed in.
Compare Symbolics Genera to a Free Software Common Lisp development environment today (SBCL and SLIME on GNU Emacs). The latter does a lot less and is more bloated. Commercial Common Lisp compilers like Allegro and LispWorks have features and optimizations that Free Software compilers lack (Allegro has really good debugging tools and garbage collection, LispWorks has excellent support for concurrent programming).
Intel Fortran compiler and their C++ compiler produce the fastest code. Lucid Energize and IBM VisualAge C++ did incremental compilation and had IDE features not available with Free Software C++ compilers and editors/debuggers.
Genera ran on actual Lisp machines, I feel that that is not a fair comparison.
It's not exactly hidden knowledge that the Intel compilers produce the best code, it's just that they have draconian licensing requirements. Furthermore, that knowledge cannot possibly be lost, because they're still actively developed to this day. I'm interested in the technological specifics of what these older platforms did that the newer ones cannot do, and why the knowledge of how to do them has been lost.