So long as you're resetting on the first encounter, you should be ok.
The way it works is that the game randomly generates the Opposing Trainer's ID/SID and uses that for shininess rather than your own. So if it appears shiny when you battle it, it's shiny for the opposing trainer and not you. Only when you capture it will your ID/SID be applied, and then you'll see if it's shiny or not -> reset.
If you kept this up you would eventually find a shiny shadow pokemon.