Um, firstly let me explain the situation with the previous releases. They had very basic game file verification built in (few random files were selectively size-checked or even simpler: checked for presence on disk without any content checking), and thus it was comparably frequent to discover people with corrupted installations. By supporting multiple operating systems for us it is very hard to build a tool/installer that would work everywhere, and thus all the mess with the files. We believe it will get simpler when we reach EP8.
To workaround the issues at present starting with episode 5 we implemented a complete game file verification, which could unveil most of the hidden failures to properly install the game bith old and new.
Now about the game. It was and is a single game, which contains all the episodes in itself, so chiru is basically an addon you extract into the game folder (which is now mandatory). We tried to explain it at a usual place describing on how to update files, but I guess it is still imperfect:
https://umineko-project.org/en/how-to-upgrade/
Regarding the files, we try to make less changes to the larger game archives, and as a result we have several "large" game packs like backgrounds, graphics, videos… which one updates to get the latest changes. Chiru archives are one of the updates, and "extra" is an overall update that always comes last and contains the latest changes we made yet not included in the original files.
Hope it helps!