It's great that it's now possible to delete scrobbles again, thanks. I went through recent duplicates, attempting to only leave a single scrobble in each case - but deleting the duplicate appears to delete all instances, not just the duplicate one.
Although I don't have a definitive answer, I know on one of the past builds of the old sites there was a bug that would dupe scrobbles and when I deleted one dupe it deleted all of the dupes and the original scrobble. When they patched it I believe the dupes got removed with the original intact so I'd leave it be for now until the delete function is fleshed out. Annoying I know but it sounds like they reintroduced the old bug with whatever implementation they are using for deleting right now.