To set the version comment, the document needs to be checked out for version control editing, like this:

try
{
    EI.Lock(LockType.Exclusive);
    EI.SetFieldValues(FVC);
    EI.Comment = "Release Version - " + Convert.ToInt32(Version);
    EI.Save();
}
finally
{
    // Do this in a finally block to make sure the document is checked back in even if an exception is thrown
    if (EI.IsCheckedOut)
        EI.CheckIn();

    EI.Unlock();
}

To update version comments for existing versions, update them like this:

foreach (var version in doc.GetVersionHistory())
{
    version.Comment = "my new comment";
    version.Save();
}