I just downloaded and installed Windows Repair (thank you!). Since this is a new program, I ran the optional Step 2 of the pre-scan.
It found a fair number of cases of 'Missing Default Reparse Point'. I looked at these, saw that the program was correct, and manually created each of the links that were missing (using mklink /D). Now, if one opens File Explorer on this machine, one can see that each of the reparse points is correct and working. Great.
However, when I ran Windows Repair, again after having made this fix, it still reports the reparse points as missing. This is really odd since they are all there and they all work. Since I suspect that I did stuff correctly, it is possible that this is a bug...