The Patch
In February of '97 Lucas Arts released a patch called Yoda Update #6 that fixes problems in some zones. The Patch is a self-extracting archive that replaces the main game data file Yodesk.dta with a new one.
A prompt saying zones #72, #236, #407, #474 and #572 have been fixed appears when the update is run.
The original release notes of yopatch6.exe have been preserved by the Wayback Machine here (and with a different design here). They claim that in addition to the zone fixes "minor art modifications" have been made.
It would be interesting to find out what exactly has changed in the newer data file.
$ shasum yopatch6.exe
a8e18864184d49feaf0b74b93f60855f40ffe9bf yopatch6.exe
$ file yopatch6.exe
yopatch6.exe: PE32 executable (GUI) Intel 80386, for MS Windows