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Qenya was the early name of the High-Elven tongue which gradually would change into Quenya of the Lord of the Rings. In the earliest versions of the legendarium Qenya was the language of the First Tribe of the Elves, the Lindar (Vanyar in the later legendarium).
During that time, Tolkien used to write the sound [kʷ] simply as a single q. Therefore the name Qenya is still supposed to be pronounced ([ˈkʷeɲa]). While writing the Lord of the Rings, Tolkien decided to adopt the romanized spelling qu both for aesthetic reasons, and to accentuate the role of Quenya as an "Elf-latin". This does not alter the pronounciation.
Since the High-Elven language changed throughout Tolkien's lifetime from its conception until late in his life, the spelling "Qenya" (without "u") is used by Tolkienists and linguists to differentiate the early version of this language. Helge Fauskanger used to refer to that stage of Quenya as "immature" in order to make clear that he refers to Tolkien's point of view and not an early historical stage of Quenya, as in ancient Quenya of Valinor. However the term "immature" was considered controversial and derogatory.