Now that Mother's Cookie Company, Inc. has been sold off for its assets, who now owns the intellectual property of the cookie recipes?

Kellogg Company acquired both the Mother's trademarks as well as the recipes late last year.

Here's an official Kellogg's press release that says as much:
link

This is good news for fans of Mother's and it will be great to see many of these classic biscuits, cookies reintroduced at some point with the original recipes (hopefully) intact.

Put that cookie down! NOW!