O.K. this may seem like a dumb question , but does anyone know the algorithm to fix the 4x4 parity where two adjacent edges are flipped. Sorry if this has already been disused and I just missed it, but the only algorithm I could find was the one for two opposite edges. Thanks for the help everyone.

When you use the term "flipped" I assume you mean swapped because neither of the cases you described are parity cases, they are normal 3x3 occurrences. swap the two adjacent edges, just apply the algorithm that is given for the two opposite edges, then solve like a 3x3.

good luck!

Sorry about that I did mean swapped. So your saying that there is no algorithm for the case I described.

I believe there is, but I don't know it, and its not required to solve the puzzle.

Hold the cube so that the two swapped edge pairs are on the front and right sides of the top layer. Do (R B) to get one of the edge pairs to the back face. Now they're opposite. Then do the move that you know already to swap the edge pairs. Then reverse the two setup moves (B' R')
Hope that helps. Let me know if you dont understand.

Got it thanks. I love when simple solutions work.

Bump! When I do that settup move, then do that parity alg, it leaves me with 2 edges FLIPPED, and then i have to do the OLL that I know that does not change the permutation. Is there a way of having a different setup move?

To swap the edge pairs at UF and UR, do R U R' U' (parity alg) U R U' R'.