Absolutely. All of Lara's scenes in the FOS in II originally featured Jor-El. The producers had Richard Lester reshoot all of Brando's scenes with Susannah York (Lara) so they wouldn't have to pay Brando for II. Sadly the most important Brando scene in the film which was cut and never reshot (I always wondered about that) was the scene you mentioned.
After Clark finds out about Zod taking over the planet and returns to the Fortress and finds the green crystal, Jor-El appears to him one last time. He commits spiritual suicide in a sense to give Clark back his powers (those were the consequences for Clark turning his back on the world, to be with Lois). Superman got his powers back to save the world from Zod, but at the price of the communication link between him and his father was lost forever.
In the Theatrical Cut, the scene ended right after Clark finds the green crystal and we never saw how he got his powers back which left a huge plot hole in the middle of the film. Fortunately, all of Jor-El's scenes have been reinserted into the Donner Cut, which comes out later this year.