The Star Trek TAS episode 'More Tribbles More Troubles' was released on TAS Complete Series Disc 1 and on TOS-R Season 2 Disc 5.
The Star Trek DS9 episode 'Trials and Tribble-ations' was released on DS9 Season 5 Disc 2 and on TOS-R Season 2 Disc 5.
The X-Files episode 'Millennium' was released on X-Files Season 7 Disc 1 and on Millennium Season 3 Disc 6.
The CSI episode 'Cross-Jurisdictions' was released on CSI Season 2 Disc 6 and on CSI Miami Season 1 Disc 1.
The CSI episode 'MIA/NYC Non-Stop' was released on CSI Miami Season 2 Disc 6 and on CSI NY Season 1 Disc 1.
Can anyone think of any more examples?