The aforementioned Clip Show episode for the aforementioned reason.
"How's Bayou", well, sorta... There were two versions of the episode. The original was never completed, due to time constraints, but when the series was picked up for syndication, a second, more common version was shown with additional scenes and dialogue to keep the storyline in place, but with other dialogue taken out as well. Only the original was included on the DVD set, and the more common syndicated version is nowhere to be found in that set.
Almost all of the opening teasers save for the first episode and some season three episodes are gone in the DVD sets. Depending on who you ask, either they were not part of Shout! Factory's deal with DIC Entertainment, or they were accidentally destroyed by Disney during DiC's short tenure there.
Screwed by the Network: While NBC gave Captain N fair treatment for its first season, its second and third season became the target of network politics as NBC began to move away from its Saturday Morning block. The third season in particular was noted for the removal of many licensed characters (except those from Nintendo), shorter episode length, dialogue changes and shift to cheaper animation studios. NBC canceled the program without warning after this final straw (its pairing program, Super Mario World, also suffered this fate), and its timeslot was returned to the affiliates once the 1991-1992 television season ended. The affiliates promptly replaced the show with additional local news. The show suffered this in its final two seasons as NBC began phasing out their Saturday morning block. First, NBC stopped promoting the series from season two onwards, meaning that viewers would have to rely on word-of-mouth in order to not miss a new episode. Second, after season three was renewed, NBC drastically cut the show's production budget in favor of a superior performer, Saved by the Bell, causing the quality of the show to deteriorate and prompting audiences to stay away. Finally, once the abysmal ratings for season three came in, NBC halted production of the show, along with all other animated programming, indefinitely, putting it and other programs in reruns for about a year before ditching its Saturday morning block completely, effectively canceling Captain N. Its timeslot was later replaced by local news.