There have been no reported changes to the API, officially for many years, (unofficially since January).
But, frankly that script's approach should have never worked. OAuth credentials are sent to:
https://stackapps.com/a/7936#access_token=y6rVASxxxxxxxxxRO2R9Bg))
(for example)
But this is immediately 302 redirected to:
https://stackapps.com/questions/7935/bulk-flag-comments/7936#7936
So the current script cannot see the access token. (Except maybe on a really bad network/system, but one shouldn't count on such things.)
Anyway, You should never OAuth redirect to a page that is not fully owned and controlled by yourself, and on your server -- unless it is the officially provided URL for client side OAuth.‡
For the Stack Exchange API, this URL is: https://stackoverflow.com/oauth/login_success
.
See this answerthis answer on Meta Stack Exchange for framework code and an example of using authentication with a userscriptframework code and an example of using authentication with a userscript.
‡ Not only is that brittle (as you have discovered), it can also be a major security risk, depending on the page chosen.