Nothing vanishes, unless you keep calm and use --force in pacman. From pacman.conf:
HANDLING CONFIG FILES
Pacman uses the same logic as rpm to determine action against files that are designated to be backed up. During an upgrade, three MD5 hashes are used for each backup file to determine the required
action: one for the original file installed, one for the new file that is about to be installed, and one for the actual file existing on the file system. After comparing these three hashes, the
follow scenarios can result:
original=X, current=X, new=X
All three files are the same, so overwrites are not an issue. Install the new file.
original=X, current=X, new=Y
The current file is the same as the original, but the new one differs. Since the user did not ever modify the file, and the new one may contain improvements or bug fixes, install the new file.
original=X, current=Y, new=X
Both package versions contain the exact same file, but the one on the file system has been modified. Leave the current file in place.
original=X, current=Y, new=Y
The new file is identical to the current file. Install the new file.
original=X, current=Y, new=Z
All three files are different, so install the new file with a .pacnew extension and warn the user. The user must then manually merge any necessary changes into the original file.
original=NULL, current=Y, new=Z
The package was not previously installed, and the file already exists on the file system. Install the new file with a .pacnew extension and warn the user. The user must then manually merge any
necessary changes into the original file.
Why don't you rankmirrors your mirrorlist?