SAN FRANCISCO, Sept 4 (Reuters) - Amazon.com Inc AMZN.O said it would replace copies of digital books that it purposefully deleted from its customers' electronic readers this summer, as the online retailer sought to make amends for the controversial incident.

In an email to the affected customers on Thursday, Amazon said it would provide owners of its Kindle electronic book reader with new copies of the George Orwell novels 1984 and Animal Farm for no charge.

Amazon said customers could also choose to receive a $30 gift certificate or check instead.

The email also contained a copy of the apology that Amazon CEO Jeff Bezos made in July, in which he called the company’s deletion of the books “stupid, thoughtless and painfully out of line with our principles.”

In July, Amazon acknowledged that it had deleted the Orwell e-books from the Kindles of an undisclosed number of owners. Amazon said it deleted the books because it learned an outside company had added the books to Amazon’s catalog but the outside company did not have the rights to sell them.

The move triggered a wave of criticism on the Internet, and Amazon was sued by a high-school student who said Amazon deleted his copy of 1984 and the “copious notes” he had taken on the book.

Amazon’s email on Thursday said that the company would replace the deleted books along with any annotations made by customers.

Amazon spokesman Andrew Herdener said the move was unrelated to the lawsuit, and said the company does not comment on active litigation. (Reporting by Alexei Oreskovic; editing by Carol Bishopric )