So the name for the island on which the events of my story exist is called 'Epistyl.' Out of a lack of anything to call it at the time... and since, I stuck a placeholder name of 'Epis' on the capital of the community. My girlfriend, a.k.a. my proof reader has grown accustomed to this name now and didn't really want me to change it. I want to rename it something like 'Epsilon' like the Greek letter so that it is easier to differentiate between the island and capital. what are your thoughts? Epis or Epsilon?
Hate to not be of any help, but I think either one is fine. For me the -styl at the end of the island's name is sufficient differentiation.
But Epistyl reminds me of Epistles, which is a real word lol. It also reminds me of "A pistol". Epis sounds like "a piss" to me, sorry... that or Epic In general I like none of those names. But in the end, it doesn't matter as long as you like it. I wouldn't keep it just because your girlfriend wants it - she'll get over it I'm sure!
It is pretty common for cities to take on the name of their country or have similar names, even in real life: New York City, New York and Oklahoma City, Oklahoma are two examples. I think you are fine with leaving the names as is.
Do what you want to do. If you want to go with the Greek letter thing do it. Personally it would be helpful to the reader if you did Epis I believe simply, because it's easier to identify a shorter word from a longer one. If you did two long words I feel it would just be confusing :S