Hello, I own a server that use custom texture packs, and it is using BungeeCord (Hub proxy by md_5). I need the texture to reset to deafault on some servers like the hub, so I uploaded a texture pack with just the pack.txt on my webserver. When player join, they need to accept the server for the whole server. When they accept, the chunks don't refresh. Placing/breaking block updates the chunks and fixs the texture for that single chunk. I can update the chunks using Bukkit ATM, which is a temp. fix. He is some example.
I tested this with Minecraft Server Vanilla. My client is vanilla as well.

Also, if a player force updates the chunks (F3+A) is fixes itself. I way to fix this is to make the player update the loaded chunks a couple ticks when he finishs downloading a texture pack (5 ticks works fine).
Finally, if you would like to test it yourself, email me at craftthatblock@gmail.com to get the IP.