First off, to prevent making this mess again, remember the Eagle rule - ALWAYS keep BOTH editors open. As long as both are open, any change you make on the schematic is automatically made on the board, and they're kept consistent.
Now, to fix your problem.
If the only thing you've done since the schematic and board were last saved in a consistent state was to rotate a connector, it might be easiest to close Eagle, replace the schematic only with the previous backup version, then open Eagle and make the change with the board editor open too.
If you don't want to do that, you need to fix all the errors until Eagle is happy. Judging by the error reported, I'm guessing when you say you "rotated the connector", you also swapped the pins around to connect more neatly? If so, that's why it's not consistent. With both editors open, swap them back on the schematic, re-run ERC, and if you're lucky the errors will have gone and consistency restored. Then you can swap them again.