Here is how to fix mismatching symmetry or mirroring in Mudbox.
First bring your model down to the lowest 0 subdivision level. Then change your tool in the bottom go to select/move tools. select the "faces" tool
Hit "w" to turn the wire mesh on your model on.
Select a face on one side of the center axis then on the other.
Then in the top menu go to Mesh>Set Topological Axis (in mudbox 2014 they moved this to the Edit menu)
You may get a message at the bottom saying that the symytry was not initialed becuase it wasn't a full quad mesh and that you need to repeat the last step on the next subdivision level. If you see this message just hit "page up" to go to your next sub level 1 and go to Mesh>Set Topological Axis again. It should work this time.
Now go to the subdivision level and layer you want to fix your symmetry on.
With the faces selection tool just select some random faces on the side of the center axis you want to take the mirror FROM and then right click the sculpt layer in the list and choose "Mirror X". Immediately it matches the symmetry to the opposite side.
Do this with any sculpt layers that you need to match up. That's it!
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