Yes, please try to replicate this with the latest beta. If you can still get your config file to be long I'll look into this and hopefully resolve it for the next release.

If you can get it to "lose" the configuration, I would be interested in whether your phex.cfg is missing, empty, or with some values missing.

I can think of one way the config file could be broken: if you run out of disk space. Could this have been the cause? Obviously, if there's no space on disk Phex will not be able to create a new file. I'll look at the code and confirm this is a possibility. The workaround would be to not delete the old config until the new one is successfully written. Perhaps the code is doing this already, but as I said, I haven't checked it yet.