Yes, you can clear the configuration on the filesystem by running the {"cmd":"reset_to_factory"} command in Various Console Commands · particle-iot/tracker-edge Wiki · GitHub.
Some advice on debugging the crashing problem may be to separate the configuration into another function. I have noticed that several ConfigObject instances residing in the same place may consume a bunch of space on the stack and cause an overflow. We'll work on a different way to setup these objects so that the stack isn't used up in the future.