If the telescope was pointing correctly before the flip but not after then it looks like an issue with how the mount handles pointing on either side of the meridian. This could be what's called cone error, and is the amount by which the optical axis of the telescope is not orthogonal to the Dec axis.
The way that most of the difference is in declination supports this, the difference of 15.7 degrees could imply a cone error of half that - 7.8 degrees.
You should be able to test this manually. Slew to an object really close to the meridian, center it in the EP and note the Ra and Dec values the mount reports.
Then do a pier flip manually, setting the mount to the same coordinates but on the other side of the pier. It should be pointed differently and if you centre the same object you should see that the Dec value in particular is different.