Proper Naming for Properties Representing Strings Starting with Numbers

An object-oriented design may actually be appropriate here, but both your parse methods belong in separate subclasses. You can use generics (type parameters) to achieve this. Something like:

interface IParser<T>
{
    public T parse(string);
}

class SomeParser : IParser<int>
{
    public int parse(string file)
    {
        ...
    }
}

class AnotherParser : IParser<string[]>
{
    public string[] parse(string file)
    {
        ...
    }
}

My C# is rusty, hopefully I haven't glossed over any language constraints.

I would implement UpScript and DownScript as interfaces that have the same members:

public interface IUpScript {
    public long Version { get; private set; }
    public string Name { get; private set; }
    public string Content { get; private set; }
}
// ...
public interface IDownScript {
    public long Version { get; private set; }
    public string Name { get; private set; }
    public string Content { get; private set; }
}

This approach attempts to provide the minimal code needed to create a distinction between up and down, nothing more. Thoughts:

• Classes implementing an interface will have the common properties you've defined as in your other approaches but don't inherit implementation details like a constructor.
• Your implementing classes would be free to extend other classes if they needed.
• It looks as though you don't need to support multiple implementations of up and down scripts but you'd have no trouble doing so.