The answer is always, it depends. First of all, try to guess how much time they have invested in the comments. It takes time to read material and give feedback, and time is in short supply at most agencies and publishing houses. I have seen an almost identical letter sent to two authors about two different books. Both authors had thought they were detailed, personal letters - I thought the first one I saw was personal too - but they weren't, so watch out. Can you pinpoint evidence that shows they have really read your novel through and are making specific comments regarding your work, or is it just some clever stock phrases and generalisations?
Secondly, if you decide that it is a genuine response, are they spotting problems, or suggesting solutions? Suggesting that Clarissa might have received a letter telling her that Jack is a double-crosser is a solution, but do you know what they think the problem is? If Clarissa believes Jack to be a traitor, that will colour her relationship with him and make it more conflicted. So, is the problem that her relationship with Jack is too easy and straightforward? If they're suggesting solutions, work out what you think the problem is first. And then decide if you agree with it.
I feel very strongly that it is the writer's job to find out their own solutions to the problem. Others can make suggestions, which might inspire you, but it's your writing. When I work with my editor she makes suggestions, but I'm always trying to pinpoint exactly what the problem is. Then I can solve it in my way.
But that's working with someone who has already paid for the book, and therefore has a stake in it, which brings me on to my third point. You don't have to do anything. Yes, you want to get an agent or be taken on by a publisher, but you don't have to jump through their hoops if you don't want to. And I would be very wary of leaping in and making changes on the basis of just one letter from someone who hasn't paid out any hard cash.
Talk is cheap. You could spend weeks re-writing your book for someone who still turns it down. You might then have to re-write it for someone else who sees different problems. I have seen students re-write several times and end up so thoroughly confused that they've ditched the novel. Hang on to your own sense of what you're writing and why you're writing it, and make sensible decisions about re-writes that work for you.
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