Even a 990-PF return that is amended must be made available for public inspection. You must have the return available for inspection for 3 years from the date of filing or 3 years from the date the original return was due.
If the organization files an amended return to claim a refund of the tax amount paid under section 4940 or 4948, it must file the amended return within 3 years after the date the original return was filed, or within 2 years from the date the tax was paid, whichever date is later.