Debugging with external files and alternate load methods

I'm working on an application that has two load methods. One method is called when the user clicks the load option. The other uses command line arguments, so that a file associated with my program can be opened directly. Recently, I decided to update the file and folder structure for compliance with the program. Loading from with the load option works perfectly, but there is a bug loading with command line. Now, I'm stuck with the problem of trying to debug something that cannot be run from inside the normal debugger! Does anyone have any information that could help me debug the command line argument load method? Thank you in advance.