On UNIX/X11 (FreeBSD, Linux and Mac OS X) you can use the --uninstall command line argument to reset application settings. Run this from a terminal:
PixInsight --help
for a complete description of all command line arguments available.
On Mac OS X and Windows you can also launch the PixInsight Core application with the Ctrl key pressed to trigger the same uninstall mode. Note that this does not work on FreeBSD and Linux since build 1087 (X11 issues).
On Windows, the installation program creates a "Reset PixInsight Settings" entry on the "Start/PixInsight Platform" menu (or whatever replaces it on Windows 8).