Update, following it through the issue seems to be caused by the fact that the data is dodgy when UClass::Link is called. In my current build it gets called no less than 11 times for changing the 1 class, multiple times for each of SKEL_myblueprint, REINST_SKEL_myblueprint, myblueprint and REINST_myblueprint.
The REINST_ versions seem to be the old versions of the blue print classes. They derived from HOTRELOAD_ versions of my c++ class, which appear to be the old versions of the c++ class. However, these HOTRELOAD_ versions have a NULL pointer for their ‘Children’ linked list. As such, the link function assumes the old c++ class has no properties.
Throughout the process the linking also occurs for the new classes, and in these cases they do have a pointer for their ‘Children’, and thus the link function detects the super class’s properties correctly.
I have also verified that the old HOTRELOAD_ class definitions are still invalid at the point at which the CopyPropertiesForUnrelatedObjects is called.
Thus I assume the issue is that the Children pointer is being unnecessarily cleared.