On a recently designed board, I used the renumber components feature in PCB design and then performed back annotation of the schematics.
All the components were correctly renumbered in the schematic, except for some of the power symbols connected to components.
Oddly, they assumed the reference designators of the IC or component they were attached to.
As an example, +12V and -12V were attached to two reverse polarity protection diodes where power comes in to the board.
After I performed the back annotation, I had D1-D4 with the power symbols as D3 and D4. The same was true of power to one IC. After back annotation, the +12V connected to that IC had a ref designator of U12 (the next unused "U" ref des).
This did not happen with any other power connections. I went back and checked the properties of the power symbol, but could not find anything wrong with it.
Unfortunately, this is a previously unreported fault. Would you email me with as much information as you can. A backup of the design before it went wrong is a bit too much to hope for, but the design in its current state including the back annotation report would be helpful.