"a separate version" is correct and usable in written English.
You can use it when referring to two or more versions of something. For example: "I have a separate version of the document with my revised changes."
There was, in the history of illustration, a thing called color pre-separation, in which artists drew a separate version of every drawing for each color of ink to be printed.
Now there's a separate version optimised for the Etymotic Pro headsets.
Each update to a file may be stored as a separate version, to reverse unwanted changes.
For Columbia University Central Administration areas there is a separate version of the Spider software for centralized SSN scanning.
The GGSC is also planning to create a separate version of Thnx4, called Thnx4Schools, for use across entire school communities and with students.
Rival studio Warner Bros has hired mo-cap king Andy Serkis to make his directorial debut on a separate version now expected in cinemas for 2017.
WordPress, itself, and all plugins and themes are uploaded to a separate version-controlled repository, then deployed via scripts to the QA and production web servers.
A separate edition of the Wadding version of De modis significandi was printed in Garcia 1902.
Recently, Capcom released a new separate version called Resident Evil 4 for Beginners, which offers the first two levels (three counting a training level) of both Story Mode and Mercenary Mode.
Also, based on the American English version, a separate English version for use in the U.K. was developed, following changes to the language, grammar and style.
If you do end up using a separate mobile version of your site, you'll want to ensure complete equivalence between your two versions.
