I have bought fm modulators two time in two days (replaced second time) both lasted 5 minutes in the car... personally I will say get rid of the modulator all together :)...
The file system get corrupted because there is no voltage stabilizer inside, as the car starts it probably send some high voltage to the modulator and it screws the file system of the USB... you can however practice taking out the modulator every-time you turn off the car and putting it back in AFTER you start the car.
The file system can be recovered by a simple "Format" through the computer I think.