I did not, but one of the lost pokemon was my first shiny, so "no" is not an option here. We are in "actively call Nintendo support and cry over the phone at them" territory here. I'm willing to physically cut the cartridge open if it might work. I'm willing to break into the turtle file and see if it keeps a record of the Pokemon transfered out to main series games (side note, what's the deal with turtle? why is it even called turtle?). There's gotta be an option.
Guess who just manually recreated every legendary and shiny FROM MEMORY?
Suck it, past me.