As I suspected it was my fault-a clerical error. Some time before the update, I somehow did something that produced the FlightSim2020 folder. When the update asked for the root directory, I did not browse for it, but carelessly accepted the default. Unfortunately, it was not the root but something with the same structure. The update then updated it rather than the root. The result was a106GB folder structure that was fully operational except for the lack of all but two aircraft. The fix was simple. I backed out the installed mods (with the MODMANFX a trivial operation), deleted the FlightSim2020 folder and ran the update again with the correct root. Everything worked fine.
As a postscript, I believe that the folks at http://www.msfsaddons.org are by-and-large competent and vet their mods before posting them. Many have been producing mods for DCS and FSX for a while. Both of these simulators were once new. A few pioneers must bleed until the community trusts their work. Perhaps I am foolhardy for trying to use their products at this early stage, but I felt the risk was worth the gain.
To appreciate the quality of some of the mods, I suggest looking at the VL_3 915 community project. One has to be impressed with extensive planning and execution exhibited.
All of the mods were reinstalled using MODMANFX and are happily chugging along. They have caused no problems whatsoever and make an appreciated addition to my simulator.