Start off by not using Split - it probably won't help that much. The way I would do this is to work out where the "root folder" that holds the file is, and use String.Replace to change it. For example:
string basePath = @"D:\Temp\MyPicturesAreHere";
string newPath = @"D:\NewFolderForFiles";
...
string originalFile = @"D:\Temp\MyPicturesAreHere\A Folder\Another Folder\A File.js";
string newFile = originalFile.Replace(basePath, newPath);
Console.WriteLine(newFile);
Would print:
D:\NewFolderForFiles\A Folder\Another Folder\A File.js
Which is what you seem to be looking for.