I work at a company that uses 3dsMAX to work on individual medical related jobs. We work on between 40-50 jobs a day, and are constantly importing and exporting .stl files. Is there a way to default the import/export function to a main hard drive, so that there is no risk of overwriting files?
I ran into your same problem with Max 2011 recently, when I decided to setup a project I was working on the way it is suggested in the Max tutorials. With this setup, when you start the project, Max sets up all its' usual folders in the directory you specify (scenes, import, export, matlibs, etc.).
It worked great for that particular project, but I then noticed that my next project, for a different client, was trying to save in the last
project's directory. So I once again set the preferences for the new project folder. Not the greatest solution.
I think, though, that all you have to do is set your preferences to be the folder in which you want all of your .stl files to live, and from then on, it will default to that folder (say "import", for example). Does this make sense? I know that it won't help with where your files are prior to the change, but then maybe you could move and relink the existing files so that they will link properly.