Once they’re found, they’d be handled by the Obliviators.
It wouldn’t be a problem if there were a few Muggles who left New York and didn’t come into contact with the Swooping Evil venom in the rain. There would be a much smaller number of them, so they can be handled in the typical way. Usually, the Obliviators handle the Muggles who witness magic. The only reason they couldn’t after the Obscurus wreaked havoc throughout New York was because there were simply too many people who needed to be Obliviated for them to feasibly handle - there was an entire densely populated city of Muggles they’d have to Obliviate.
“MADAM PICQUERY
We owe you an apology, Mr Scamander. But the magical community is exposed! We cannot Obliviate an entire city.”
- Fantastic Beasts and Where to Find Them: The Original Screenplay
When it’s not the entire city of New York, when there are Muggles who witnessed magic, the Obliviators are able to handle it. They can manage fairly large numbers of people had Obliviated all of the Second Salemers after Tina used magic on Mary Lou Barebone in front of them.
“NEWT
(realising)
And she was the No-Maj you attacked?
TINA
That’s how I lost my job. I went for her in front of a meeting of her crazy followers – they all had to be Obliviated. It was a big scandal.”
- Fantastic Beasts and Where to Find Them: The Original Screenplay
The Swooping Evil venom Obliviated the vast majority of Muggles who needed to be - MACUSA would just have their Obliviators handle anyone who was somehow missed by the venom.
A few might not get Obliviated, but they’d be thought mad.
It is theoretically possible that MACUSA could miss a few stray Muggles and not Obliviate them, but even if they did, those few would be thought mad by other Muggles and dismissed as lunatics. Newt himself mentioned this in his book Fantastic Beasts and Where to Find Them.
“There can be no doubt that the overwhelming majority of present-day Muggles refuse to believe in the magical beasts their ancestors so feared. Even those Muggles who do notice Porlock droppings or Streeler trails – it would be foolish to suppose that all traces of these creatures can be hidden – appear satisfied with the flimsiest non-magical explanation.8 If any Muggle is unwise enough to confide in another that he has spotted a Hippogriff winging its way north, he is generally believed to be drunk or a “loony.”
- Fantastic Beasts and Where to Find Them
Even if MACUSA missed a few Muggles, those few Muggles wouldn’t be believed, they’d just be considered lunatics by the Muggle community, and the existence of wizards would remain secret.
