Well, keeping fingers (legs, elbows, eyes and toes) crossed.
RTMM reg. scenery all re-installed and appears to work. Scenery Tester shows all objects correctly which it did yesterday and today I had to re-install two Libraries to get them all showing again, go figure!
Still have some of the special stuff, Hawaii, CIRP etc. to put in but for now I'm going to give myself a birthday present and a rest all at once and fly for a bit before starting on more installs.