from the instructions at IRS:

If your 990-N is late, the IRS will send a reminder notice to the last address we received. 

While there is no penalty assessment for filing Form 990-N late, organizations that fail to file required Forms 990, 990-EZ or 990-N for three consecutive years will automatically lose their tax-exempt status. Revocation of the organization’s tax-exempt status will happen on the filing due date of the third consecutively-missed year.

Link: https://www.irs.gov/charities-non-profits/annual-electronic-filing-requirement-for-small-exempt-orga...