I've overlooked the Invisible condition description for years.
Looking at the spell Invisibility: (emphasis mine)
A creature you touch becomes invisible until the spell ends. Anything the target is wearing or carrying is invisible as long as it is on the target's person.
Invisibility grants the "invisible" condition, but what exactly does "invisible" mean in 5e? (Emphasis mine)
An invisible creature is impossible to see without the aid of magic or a special sense. For the purpose of hiding, the creature is heavily obscured. The creature's location can be detected by any noise it makes or any tracks it leaves.
So, in the case of tossing flour on an invisible flying object, this is not "aid of magic" nor would a theoretical Flour-Vision be a "special sense"
So I'm now relying on Noise detection, or any tracks it leaves.
Per the Invisibility spell description, "Anything" the target is carrying (now flour which is being carried similar to the target's clothes) is invisible so long as it is on the target's person.
So is the flour now invisible due to the Invisibility Spell? Does it even matter since the flour is not magical aid?
If the target being hit with flour was on the ground, you could say that the footprints not covered in flour would be seen as tracks, but for a flying creature, there will be no footprints.
This has been discussed a little in: Overcoming flour or other nonmagical ways to defeat invisibility but the question was closed due to being opinion based rather than looking at rules specifically.
It doesn't have to be flour specifically, but trying to tag an invisible creature with an arrow and other scenarios, some of which wouldn't even leave a trail on a standing target, though the sound of impact may work in some cases.
