I've just returned to this game after a couple years off, so I'm far from an expert, but I'll take a whack at a response since no one else has an answer.
I do most of my price management from the "manage routes" screen by using the quick "manage prices" $ button on the right side which uses a popup. I have noticed that if I change a price and "confirm," if I immediately try to "manage prices" via this button again, it shows the old price. Refresh the manage routes screen before clicking this and that problem goes away. It will show your adjusted price.
Every route has a destination and return price. Try changing the prices directly from the "route information" page. Make sure to "SAVE
" (The button will show up after you click in the price box.)
When viewing from the Price Management>Route Pricing page, only the destination price is shown. For example: my flight DTW-ATL
SU001 Y: $ 279, C: $ 799, F: $ 1 099
$279 is my price DTW-ATL (SU001), but I have $289 for the return flight ATL-DTW (SU002)
So, if for some reason you were able to adjust one flight but not the other, you are not seeing the WRONG price, but you are seeing only HALF the picture.
Additionally you can change the price from the Price Management>Route Pricing page using the "route pricing-update route" box at the bottom. Just make sure you check the box to "update also return price" or you may see half the picture again.
Beyond the popup quick $ Mange prices button in the manage routes screen, the pricing features have worked perfectly for me.
I hope you get the problem worked out and you are able to raise your prices on the DTW-PHL routes.
Maybe I'll gain a little market share!
Edit: I can't see that you've you done something wrong by what you wrote, so if you continue to have issues, you might want to bug report using the forum thread for that stuff.