My overlays disappeared all of a sudden (or so I thought). I came across this article https://corengen.wordpress.com/2014/07/30/my-tortoisesvn-icon-overlays-have-disappeared/ which points out that windows has 15 slots for overlay icons; 4 are reserved for windows, which leaves 11 for other applications. Regardless of how many overlay keys are in the registry, Windows selects the first 11 in alphabetical order.
When I upgraded Office, OneDrive added overlay icons -- prefixed with a lot of spaces -- pushing down Tortoise's overlays below the threshold: windows registry Since I am not using OneDrive, the solution was to add a "z" to the OneDrive key names.