Hmm, no, it doesn't. Maybe there's something related, for example, have the Designators all been cleaned up and placed right-ways-up or are they flipped? Try turning on the Comments, see if they are mirrored?
Example: if I flip this part, the designator and comment become mirrored. If I fix the designator, everything looks fine, but the pads are still swapped. But if I select the component, select the Comment (in the Inspector Panel), and optionally un-hide it, I see it is still mirrored.
You can use the Filter Panel with:
IsComment AND Mirror
to select the comments, then select the components/owners by following the link in Inspector. You'll have to place everything again, because I don't think there's a way to flip them in place, other than dragging each and pressing X. But all the routing is wrong anyway, so you were probably expecting that. (You can save placement by copying the X/Y positions in PCB List, doing the flip, going to edit mode, and pasting them back in.)
Tim