I'm wondering how explicit you are when you send an author a request to revise and resubmit? Do you always use that exact phrasing or do you switch it up a bit?
I recently received what I thought, at first glance, was an extraordinarily polite rejection. Generous praise for the writing, setting, etc, but some disappointment with the development of one of the main characters. It was specific but not editorial-letter-specific. So while Agent Amazing never used the phrase "I'm afraid I'll be passing" or anything as final as that I did take it as such. It clearly was not an offer of representation, which was the important thing in that moment.
However, when I stopped pouting and read the email again one of the last lines stuck out to me. "I'd be happy to take a look at any future revision." It doesn't seem like a clear-cut request to me, more like a casual way to suggest that it wouldn't be offensive to send it again if I felt inclined to. So, while I get that I wouldn't be bothering Agent Amazing, and while I agree with the feedback and do intend to revise accordingly, I'm not sure how to log this in my spreadsheet. And I'm not sure how to respond, either. Do I drop a line and say, "You got it, I'm on it!" or just get to work and then send it all back at the end of the summer with a, "Hey, remember me?"
You read her intentions correctly. If you revise, she's glad to take a look but she's not going to do the heavy lifting of a revision or editorial letter here.
It's leaving the door open (a good thing). This is the real deal and I'm glad you seem to understand that. (It drives me nutso to hear "I wasn't sure if she meant it!" about this kind of thing.)
You reply with "Thank you for your very helpful suggestions. I do intend to revise along the lines you suggested and I'll be back in touch when those revisions are ready for the light of day."
How you log this in your spreadsheet is you have a third category: R&R.
I have that category for writers just like you. If I've sent back an email saying something like "you need to tell me what Helena smells like in 1870" or "Chapter two is the biggest splat I've seen since Wile E Coyote met a falling safe" I keep our email conversations in a file labelled R&R.
Of course, a submission DB is a very personal thing, so you get to organize it any way you want to. I wouldn't begin to think my way is
Yes, you'll notice that all the manuscripts are numbered.
Yes, you'll notice that some of those R&Rs are long term.
Yes, you'll notice that all my email files are numbered as well.
If you're obsessive compulsive about being organized, a job as a literary agent is like Disneyland: the happiest place on earth.