Personally, I would refer to a group of Latias as just that...a "group (or flight) of Latias". Same goes with Latios. I would probably only use "Latis" if I was referring to a mixed gender flight, considering that seems to be the fan term to referring to both of them as whole.
To be quite honest, I'm more interested in what context this is going to be used in...Latias and Latios are Mythical Pokemon, which means that there aren't going to be more than one or two of them flying around in my opinion. So really, this is probably a moot point unless you are just referring to the two of them together.
I think what Eruannion is asking about is how to refer collectively to a mixed-gender group containing both Latios and Latias.
Personally, given "Lati" as a collective term for them is completely fan-made and has never been used in-universe as far as I'm aware, I'm not convinced it belongs in fanfiction, any more than something like "T-tar" or "Boltbeam". I'd just call them "a group of Latios and Latias", the same way I'd refer to a group of Tauros and Miltank or Pidgey and Spearow or some other combination of Pokémon.