In my opinion, D. longus is not dubious, contrary to what Tschopp et al. (2015) reported. It is clearly distinguishable from all named diplodocid species except D. carnegii. If it can be distinguished from D. carnegii, it is distinct from all known diplodocid species and thus valid, and if it can't, it's the senior synonym of D. carnegii and still valid. I think it can be, as D. carnegii has more dorsoventrally compressed caudal centra, but the topic probably merits further study. However, even if D. longus was dubious, the genus Diplodocus still would not be because D. longus clearly forms a clade with D. carnegii and D. hallorum.
Mike, I'm not sure I agree with your idea of the "effective type species." If D. longus had been largely ignored since the naming of D. carnegii I might agree, but while it is the less famous species it certainly hasn't been ignored, although the historical conception of it was largely based on the incorrectly-referred AMNH 223. It might've made more sense to petition the ICZN to designate AMNH 223 the neotype of D. longus, but that would've left the possibly-distinct D. longus holotype YPM 1920 nameless and so isn't a particularly satisfactory solution. If it turns out that D. longus and D. carnegii are not closely related, which strikes me as unlikely to happen, we can cross that bridge when we get to it.