I don't know if they would have qualified to file 990N; there is no late fee or penalty for that form (unlike 990EZ or 990). But if they didn't file for 3 years, that's an automatic revocation of status.

This topic has a phone number and explains the revocation and re-application process:

https://www.irs.gov/charities-non-profits/annual-electronic-notice-form-990-n-for-small-organization...