Hmm. Seems like it might be the same, but might be different; my issue doesn't seem to have to do with recency. It's just that some locations (including one folder with all my research pdfs in it!) don't seem to be getting searched. And rebuilding the metadata doesn't seem to help, even for a moment. So maybe you and I are having different issues?
I can say, now that I'm back in the office, that Alfred *does* find the folder "~/Dropbox/Pdf library". Moreover, it now, after being left alone for a week, even finds the folder "Scott, Dana" inside that folder. (I've made no changes of any sort on this computer; nor have I modified that folder in the dropbox, although I have made other changes in the dropbox. Spotlight reported that the metadata was already fully rebuilt before.) But Alfred still does not find very many folders inside "~/Dropbox/Pdf library", and it does not seem to find any pdfs inside any of these folders, whether or not it finds the folders themselves.
I hadn't tried Houdahspot before, but after installing the trial, I can confirm that it exhibits the very same gaps in coverage that Alfred does. Spotlight finds everything fine, and Alfred and Houdahspot both seem to succeed on some things and fail on others, matching perfectly as far as I can tell in what they succeed and fail on. That certainly does seem like relevant information!
Anyhow, I've sent the diagnostic email as requested; hopefully it helps! (But I also misspelled your name, Vero, in that email; I'm sorry!)