Which downloads are you using? If you're on Windows, it either sends you to Google Drive, or Mega, which shouldn't be blocked, unless you're on a network connection that restricts what you can access, such as school wifi.
Here's a general tip: Dont teleport. There are many events that are tied to specific tiles, timers, variables, and switches. If you miss any of these, or interact with the wrong event, you will sequence break your game, and be softlocked.
I do not have a copy of E5 to test your save. If you've just updated to E6, you most likely will have to restart your game anyways, due to it being an incomplete run of the game.
PBS files have changed with the recent update, and are no longer required. You can edit everything through the scripts now. File path \Desktop\Pokemon Desolation\Scripts\Pokemon Desolation
RKS System changes it's typing to ??? on the Glitch Field, however it should have reverted after. Try throwing it into battle, or throwing a memory on it, and see if it reverts back to normal.
This is most likely due to your save file not being converted to E6, if it was an save from E5, please follow the conversion process, shown on the download page.