Simple C# application that transfers new files (modified in the last 24 hours) from one directory to another
A few notes, not in order of importance, just as I see them. Keep in mind this is just my opinions but I think they're important especially since you're starting out. You can form bad habits later :)


Your classes and methods should always explicitly define their level of accessebility. e.g. class Functions should be public class Functions
Always check if a file or directory exists before opening: var directory = new DirectoryInfo(sourceDir); should be: 

DirectoryInfo directory;
if (Directory.Exists(sourceDir))
    directory = new DirectoryInfo(sourceDir);

User input should always be compare in one case for example answerExit == "y" should be answerExit.ToLower() == "y" Unless you want to make response case sensitive.
System directories should not be explicitly entered. For example : "C:\Users\Student\Desktop\Customer Orders" should be Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop),"Customer Orders");
Your Functions class is superfluous. Those methods directly relate to activities in Main, they can't be used separately or anything else and should definitely be static.
Your method modified() return an IEnumerable and I think that this line also return an IEnumerable 

var files = directory.GetFiles()
      .Where(file =&gt; file.LastWriteTime &gt;= from_date &amp;&amp;         
      file.LastWriteTime &lt;= to_date);` So why return a .ToList()?



I think that's a good start.