miktex-portable destroys languages.ini when languages are changed (disabled) through miktex-options.
To reproduce the problem:
Make a backup of languages.ini.
In the options of a miktex-portable click on the language tab and disable one random language and click on apply/ok. Miktex then recreates the formats but these don't contain any hyphenation patterns. An inspection of languages.ini in the miktex/config folder shows that all entries have been replaced with "language attributes=" and all informations about patterns etc are lost. In language tab in miktex-options all languages are disabled and when one try to enable a language a dialog with the message "this language in not available" pops up.
Copy back the backup of languages.ini to restore the settings.
This problem appeared twice in tex.sx:
In 2012 http://tex.stackexchange.com/questions/83682/language-hyphenation-patterns-not-available and yet again yesterday tex.stackexchange.com/questions/217523/problems-finding-correct-language-dat. So I took the time to test on a miktex portable and could reproduce it.
The miktex-portable installation has only one "miktex maintained" root, so this root is "UserInstall, UserData, ...."
Ulrike Fischer
From a discussion in tex.sx (http://tex.stackexchange.com/questions/227024/error-building-miktex-format-csplain) I got the impression that formats.ini of the portable miktex has the same problem: it gets destroyed when one try to make changes with miktex settings. But I didn't tested it.
A new MiKTeX portable setup has been implemented. There are now three separate TEXMF trees for:
This will fix the issue that user settings will be overriden by the updater.