@REPYeah, that's likely a large part of it. For me, rereading these older, long favored stories, I tend the recall all the scenes which got cut most favorably, which reflects in my scores.
I understand the reasoning, yet I also have to admit, whenever I revise, I also end up removing the most memorable scenes as they just aren't as vital to the plot, yet every time I have, my readers have complained. Only, without a revision system, I have no comprehensive backups. (Well, I did, yet time does a number on most, as I've lost an awful lot of stories to hard and digital drive failures over the years. And once they're gone for good, I really have no desire to rewrite them from scratch, as they never turn out the same.
So in your case, the reads is the most important, as the scores are likely due to what's no longer in the story. So just let it go. Those scenes needed to go but don't blame your readers for preferring your originals. As that's a demonstration of your effectiveness as a storyteller. So honor that sentiment rather than lamenting it.
You made those changes for good reason, so buck up and accept the fallout and stand by, 'owning' your decision.
This is especially true for those who continually keep revising their stories, just to keep the in front of readers for the ratings. Each time I read one, I get further enraged than I was each previous time, as those 'unpopular' decisions have a cascading effect.
That's part and parcel with any revision or rewrites of older stories. Again, you either stand by your stories as they are, or you're publicly admitting they weren't that good to begin with. Which only insults for fans for their support. So these things need to be handled with kid gloves (the one's from goats, not children's winter mitts).