You probably want to save your current settings since you have a flying aircraft? If so, you should determine what version of firmware you are running. GCS pops up a version mismatch box when you connect USB. There is some button that gives you more info and it will tell you what your firmware version is.
Download and install that version of OP/LP, run that old GCS and do File->ExportUavSettings. Also, it would help you to make some screen captures of the pages where you made changes, PIDs at Stabilization page, Hardware page, Input RC, Input FMS.
Use that old version of GCS and look at this page to get the new bootloader installed.
https://librepilot.atlassian.net/wiki/spaces/LPDOC/pages/5669026/Firmware+Tab#FirmwareTab-RescuemethodMake sure you follow all instructions including after flashing booting the FC and letting it run for a minute.
Uninstall old version of GCS. Install the version of GCS you want (16.09 or next) and use this page to get the firmware installed.
https://librepilot.atlassian.net/wiki/spaces/LPDOC/pages/5669026/Firmware+Tab#FirmwareTab-ManualmethodRestore some old settings by hand or run the setup wizard.
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You can do most this with the latest version of GCS without bothering to install an old version. The new GCS will not be able to correctly save (export) or display settings from the old version of firmware though.
The file you saved that has your old settings (when you exported) can't be correctly imported with the new version, but it is a human readable text file that you can read to get your old settings and hand plug them into the new GCS.