What is an example of lost media lost due to controversy?

Yeah some scenes that were cut from Rock-A-Doodle due to concerns about being too dark for kids did resurface on Vimeo.

The Day the Clown Cried is a classic and well-documented case of this, though Jerry Lewis's own dissatisfaction with the movie is probably the main cause.

The English dub of Canadian-French cartoon Robinson Sucroe was destroyed because it turned out that the show was plagiarized off of The Adventures of Robinson Curiousity, a pitch sent to Cinar(the producers of Robinson Sucroe) beforehand:
tvtropes.org/pmwiki/pmwiki.php/WesternAnimation/RobinsonSucroe

Space Cats is also somewhat this due to it being part of the 1991 NBC Saturday Morning block... which also included Yo Yogi!, an attempt at making Yogi Bear more "hip" and "cool" with kids of the early '90s. Needless to say, the latter not only led NBC to replace the block with TNBC, but also made sure that the former would be put deep into obscurity.

A 3rd season of Little Ellen was produced, but will likely never be officially released due to Ellen's workplace abuse alongside some racial stuff she did.

I don't know how to feel that it might finally be screened when I graduate high school....

 Oh you're still in high school? interesting, i'm in my 30s. 

COVID didn't just affect Spongebob, some other shows like Cleopatra in Space had cold-related episodes temporarily unaired and not put on streaming services and older shows like Garfield had sickness related episodes temporarily removed from reruns. Personally I think it was a bit of an overreaction, I don't see what would've been so bad about people seeing sick-related episodes.

I'm surprised it took this long for Splash Mountain to get re-themed into something Princess and the Frog related given how that film came out over a decade ago, hopefully this means Disney will one day be open to doing 2-D animated films again. 

Also surprised it took this long for Mid Life Crustacean to be removed from streaming services, even as a kid I knew that episode was inappropriate back when it aired. I'm shocked Nick censors allowed the panty-raid to slip through.

I noticed like half of Salute Your Shorts is missing from Paramount Plus and other streaming services and I thought for a second that might be because of content in some of those missing episodes(some have references to the boys spying on the girls shower, one has Donkeylips going into the ladies room and getting slapped by Dina, another references those machines that dispense condoms) but then in one of the episodes that is on there(Budnick and Dina in Love Part 2) there's two of the boys dressing as Native Americans(which would definitely be called out as cultural appropriation today) and a joke about "used tissues"(usually implying someone jerked off in them) within the first 3 minutes so it's anyone's guess why those other episodes aren't on streaming.  

I know some episodes of Ren and Stimpy aren't on there for content-related reasons like Circus Midgets(since "midget" is no longer considered an acceptable term for little people)and Last Temptation of Ren/Sammy and Me(due to religious references in the former and issues with the estate of Sammy Davis Jr in the latter, both of which actually led to the episode getting banned from reruns on Nick back in the day).