As usual, the laconic pretty much covers it... a character or concept changing from one name to another for no explicitly stated reason, and no mention is made of the change within canon in an almost Remember the New Guy
-style situation. Some examples...
- Super Mario Bros. - The squid mook, introduced in Super Mario Bros. 3, was originally called "Bloober". Starting with Paper Mario, that was suddenly changed to "Blooper".
- Three from Code Lyoko:
- Due to a translation mix-up, the supercomputer was originally called the "supercalculator" in the English dub. This was later corrected.
- Kankrelats were called "Roachsters" in the first season. They were latter given their original French name.
- The fictional band The Subsonics was changed to The Subdigitals when it turned out there was a real band called The Subsonics.
- The Hitchhiker's Guide to the Galaxy - The character Zarniwoop, introduced in The Restaurant at the End of the Universe, returns in Mostly Harmless as Van Harl (he stays Zarniwoop in the radio series). In And Another Thing, he's referred to as "Zarniwoop Van Harl", somewhat correcting the disconnect.
There are bound to be plenty of others!