Hello
You can use Pokesav to make your Shaymin a Faithful Encounter, for that you just need to open your Shaymin on Pokesav and check the tag on the right-up corner (The Faithful Encounter Tag, just above the hidden hex values part).
I think that the location met does not make any difference for get the Gracidea Flower, because, to get the Flower your Shaymin just need to be a Fateful encounter Poke.