The electric parts of the dynamo hub don't care. They're an AC generator and there's no concept of reversing the flow with AC.
However, the mechanical bits of the hub itself can be a problem. You don't indicate which manufacturer/model dynamo you have. The great majority of hubs are constructed such that they are expecting the wheel to turn in a certain direction in order to keep internal nuts and bolts tightened. Going in the opposite direction could lead to fiddly bits unscrewing themselves.
Where possible, I'd try to respect the directionality of dynohubs that have directionality. It would just take an extra length of wire or some zipties to snake the power cable around to the other side, it's worth that for the peace of mind to know that the hub won't self-destruct when you're going down a long hill.
Note: All Shimanos, all Sanyo, and older Schmidt/SON hubs are vulnerable to unscrewing if they are oriented with the power leads on the left (NDS) rather than the right (drive) side. Newer Schmidt SON hubs are flippable with the exception of the SON SL (below). When in doubt, ask your manufacturer/reseller.
N.B.: Some special (and expensive) dynohubs such as the Schmidt Son SL pair with specially designed forks so that no external wires are needed, but it also means you can't flip the wheel around or it shorts to ground. Assuredly that's not the case with you.