It's still broken after all this time. The only work around I have is still a bit messy, and I'm worried that someday I erase the apps and i won't be able to download the updates.
Here's what "seems" to work for me thus far:
Run "Check for Updates", select all and then delete all from my library, but i usually "keep the files" and not fully delete completely. Then go run check for updates again, it should not show anything. Then i usually do "Check for available downloads" to see if there are any downloads, but it says none. THEN, I select the "Purchased" option under Account, and it eventually pulls all the apps that I just deleted earlier. I can click individually on every single one that is prompting to download, or if there are a lot of them, I usually can go to the bottom right corner where it says "Download All" to do most all of them together. I say "most all" because the automatic batch download stops if it hits an App that it can't download (there are usually 3 for me: Apple Books, Apple Podcasts, and Find My Friends which can only be downloaded directly on each iPhone/iPad), then I have to select the rest of the Apps individually to download the rest of them. It's messy, but it does seem to keep my library up-to-date and I can further update my iPhones/iPads from iTunes from there. Apple should fix all this for those of us loyal customers who own multiple iPhones/iPads and need to update them all together.
