I have my resourcepack hosted on a specific URL, which stays the same when uploading a different pack. I'm also sending the resourcepack packet including the hash. 

When first joining the server after uploading the new resource pack, the client detects the mismatching hashes of the local copy and the remote copy. Then Minecraft deletes the old resourcepack, and you have to rejoin to get the new one. I checked the web server logs and the client never even tries to download the pack on the first join. However, on the second join the old pack has been deleted because of the mismatch, so the new version is downloaded properly.

I attached a video below showing the process. The top left is the log of my web server. I first joined using the outdated resource pack still in the server-resource-packs directory. As you can see in the video, Minecraft just deletes the pack without trying to download a newer version. After rejoining, everything works fine.

Minecraft seems to be saving the packs using the hash of the URL as a name instead of the actual resourcepack hash.