The Codex Aureus Epternach was written in the vulgate, or German, and not the standard Latin. Latin was really the only accepted language for use in the Catholic Church until the 20th century (Donovan), so it's likely that the Codex Aureus Epternach was not used for a church or study at an abbey at all. The Lindau Gospels and Codex Aureus Epternach are probably in two different languages because they were being used for different purposes.
The Lindau Gospels were commissioned by Charles the Bald, Charlemagne's grandson, to be used in a Monastery, most likely (Lasko). Before the making of the Lindau Gospels, scripture was written in an "unsightly" form of Latin, with no spaces between words and in all capitals, which made it difficult to read and study. However, when Charles commissioned the Lindau Gospels, he had the scribes write in a new format of Latin, one with spaces between words and punctuation. This became the standard for Latin writing. The book is written in standard Latin; it was used for study at Charles the Bald's court