I had mine get corrupted the other day and had to create a new one from scratch. Mine was due to a PC lockup caused by noise.
But I've seen others lose there .xml settings, many times over the years. I don't think anyone really knows why it happens.
What I did this time is make a backup as soon as I had all my settings correct.
Another option is this program from Klaus, that will make a backup and restore you settings.
Profile comparison and port pin check