So, nothing changes for the first 35 episodes. Looks like episodes 36 (Warp Tour) and 37 (Alone Together) swap places, but other than that things stay the same until episode 46. Then things get rearranged.
Episode 46 (The Message) was supposed to air as episode 50, Episode 47 (Political Power) was slated as episode 51, which put Episode 48 (The Return) as episode 52, and episode 49 (Jailbreak) as episode 53. A few episodes got pushed to season 2, such as Episode 51 (Open Book), which was originally scheduled as episode 46. In addition, Episode 53 (Say Uncle), was going to air as episode 48. Episode 54 (Story for Steven), and episode 55 (Shirt Club) were not meant to air in that order, instead originally being episodes 52 and 54.
As for the rest of season 2, nothing more has been revealed about its order. Perhaps by the time season 1 was out, scheduling became easier. I wonder how differently things play out in the intended order?
Source 1
Source 2
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