Okay, there was a split.
Before there was only a "owncloud" package that you would install and update with apt.
But after realizing that some people don't need a database or php installed with this package because they already have theirs, the package was split in to owncloud-files ( the server core ) and owncloud-dependencies ( the required packages )
If you don't want to install / maintain / update the required packages, install the other package.
To your question - how come some files / packages were deleted: I / We don't know. It's a strange behavior but ownCloud itself does not delete anything from your system.
Hope this answer helps you, and if not feel free to ask further questions