Returned boards/cases went into landfill, keeping a few on one side for warranty fixes. Most computer industry warranty fixes use "refurbished components".

Mac128 is slightly wrong in saying that only authorised Apple employees performed upgrades. The majority were performed by local dealers, not formal employees, and nobody was counting the number of returned boards at Apple. Some leaked out into the market, hence this sort of stuff:

http://www.vintagemacworld.com/build_own.html

By the time the SE arrived, there was nothing worth salvaging in a 128K to Plus. But in the late 1980s or early 1990s, they'd be useful to the rare metal extractors.