They might be operating Not For Profit, but that doesn't make them a charitable purpose in the eyes of the IRS, since they didn't file for exemption. That means they file a tax form for what they are, such as 1065 or 1120S or 1120 or Sched C. And until they have the letter of determination, or at least an accepted application, that's what they keep filing. They might not get their approval the first attempt, either.

In the future, you should recommend they file for an Advance ruling:

https://www.irs.gov/charities-non-profits/charitable-organizations/exempt-organizations-rulings-and-...