In general, you flag the parent taxon, and leave a comment on your flag referencing the taxonomic authority that recognizes the species in question.
Be aware that iNat uses specific taxonomic authorities, however.
Not quite. 
I see from the json that you put in a species_guess, but if that ID is not recognized by iNat (for missing taxon, but can also be due to typos, an upload issue, variant spelling, poor connection, etc), it becomes a Placeholder, not an ID. Placeholders are temporary and are lost as soon as an actual ID is made.
So it wasn’t lost because someone suggested Diptera, but because it was a placeholder.