I haven’t seen any news items on this, but I did rewatch it today to see if anything had changed.
The references to Waiting for Godot seem to be intact, so it doesn’t look like those were the problem.
This leaves the references to Space Runaway Ideon (aka Densetsu Kyojin Ideon) as the culprit.
Even here there aren’t that many changes. The changes are mostly subtle redubbing, and a bit of visual touchup work.
Specifically I don’t think that the word Ideon gets used anymore, all mentions are of the nickname Idepon instead.
If I’m right then when Shimoyanagi and Endou are schooling Tarou, the names of the mecha/ships referred to were also changed. I suspect that the Kyutrowa is, or was, the Gando Rowa in the original version of Idepon Miyamori: On the Move.
I’m glad that the episode is back, and that it was salvaged mostly intact. The core messages of the episode are still there and still effective. Specifically:
- Bridging the gap between CG and hand drawn animation;
- Aoi-chan’s suitability to be a producer;, and
- Zuka-chan needing to go on with her life if auditions don’t go her way
Overall if you had to do a revision to deal with a thorny rights issue, Idepon Miyamori: On the Move is a textbook example of doing it right. Of course, not triggering the issue in the first place is better still, but I’ll take what I can get.
 Something that there needs to be a lot more of in Shirobako. 11 episodes in and Tarou is still the character that everyone loves to hate.
 Based on the Space Runaway Ideon Wikipedia page.