Oh, how horrible! My deepest sympathies. I'm glad you were able to resurrect the files.

I track submissions and publications with the StoryTracker app on my iPhone, which is handy because StoryTracker tells me when a submission is overdue for a response.

*But*, being fully convinced that any specialized software I own will die, I also keep that information in a (backed-up) plain-text file, using NoteTab Std's Outline function to separate entries. If I were still doing paper, I'd use 4x6 index cards.