[shamanNS]

IIRC the problem is down to the fact that plugin keeps only one hyphenation dictionary for Serbian language, so the one that you installed last is the one that is available to be used and thus if plugin has stored Serbian Latin dictionary trying to hyphenate ebook that is using Serbian Cyrillic alphabet will not and cannot works if dictionary rules mismatch the alphabet characters being used in a book. If you then install Serbian Cyrillic dictionary hyphenating Serbian Latin books will stop working.

In other words whenever you install Serbian language hyphenation dictionary you overwrite the already existing Serbian dictionary.

In order to hyphenate both alphabets your only choice is to reinstall the correct dictionary moments before trying to hyphenate a ebook. So, you as an user are forced to either somehow keep track of what dictionary & alphabet you used last time you used this plugin or "just" always reinstall the dictionary that matches the alphabet used by the book you intend to hyphenate.

I don't thing that even Calibre itself distinguishes between Serbian Latin and Serbian Cyrillic, as language metadata value.