Hello,
I have extensive experience in .Net, i have been in the software development industry for more than 5 years, i have been involved in the development of complex projects, worked in almost every area like desktop apps, web apps, web services, databases etc.
I am going to deliver this functionality in a WinForms application, the two files will be showed in a parent controller for each of them. My tool will maintain a file in its installation directory which will contain info about the files loaded in the tool and the lines locations in those files, this will help recognize files loaded even after years like you require, but the files need to be in same folder for my tool to remember the markers. The Html file will actually be in a parent controller and a simple button can be added right next to the selected lines, lines in pdf can be highlighted in the same way by placing small UI controls on its parent controller, let me know if you are intrerested in my solution, it shouldn't take more than 2 days.
Thank You