Take that invite and run with it! In your cover letter, explain that the owner saw the manuscript in a very different form years ago but didn’t feel it was for her. You’re not trying to pull a fast one on anybody, you’re being communicative. The owner will be fine with it. She’s been in the business long enough to appreciate how much a manuscript can change and that each agent has his/her own taste. Do one thing first, though: Check the agency’s submission guidelines to see if they specify that a “no” from one agent is a “no” from the agency. Even if they do, you’ve got an invitation, so send a note saying you’ve revised significantly and let the agent decide if she wants to read this manuscript that intrigued her. That’s being professional, not burning bridges.