I was testing the update to prevent Sigil from dragging/dropping non-contiguous files and while that drag/drop is prevented, the select of the non-contiguous files seems to work until you start the drag at which point it looks as if trying to select other files is happening.
I reverted to the release compile of Sigil 2.8.1 and tried the non-contiguous drag/drop and in 20 different ePubs, a simple move of a single or contiguous file corrected the issue in the opf file.
OTOH, I may be suffering from Friday afternoon syndrome a day early but I can't seem to spot the Edit Reading Order in the Tools dropdown menu.
Ahh... not the Tools menu but Change Reading Order in the right click menu for a text file.
As for the A/B suggested fix, I would go with A as being the easiest and least intrusive. Perhaps saving B or C for a later update.