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Updating the firmware
To perform a firmware update of one or more sticks, select all sticks you want to update by holding CTRL and clicking on them in the device tree, then right click and select "Update Firmware", which shows the update dialog. The "Current device firmware:" field shows the currently installed version if only one stick is selected.
Either load a custom firmware file (or an old version) by clicking "load form file" or simply get the latest version by clicking "get latest from GitHub". After loading it, the new firmware version number will be displayed in the "New firmware:" field.
Then make sure that you hit the midi panic button to tell the device that the music has stopped and hit "GO!". Once the software update is written to the device it needs to be restarted for the update to be installed, so click yes when the dialog asks you about the restart. The installation should take no longer than a few seconds.
The software is first written into a seperate area of flash that is not executed from, so if you get an error during the write process, all you have to do is to start the process again. However if during the process of installation something goes wrong (or the firmware that was loaded is unable to boot) you will have to un-brick the device manually.
erase settings : This can be selected if you need the settings to be overwritten with the defaults in the new firmware. this will erase EVERYTHING
Auto prog. on file change : This is used to automatically program the device if changes to the HEX file are detected. This can be used for development, if the HEX file loaded is the one that is generated by the IDE during the compilation process ({Project Folder}\dist\default\production{project name}.X.production.hex). Then all you need to do to upload the software is to hit build, instead of needing to manually hit go every time.
Auto reboot (only available with autoProg) : This will reboot all sticks automatically instead of showing the dialog. I recommend selecting this when using the autoProg feature.
Use MPLab workaround (only available with autoProg) : MPlab writes things to the HEX file a few times during the building process. Enable this option to prevent the software starting the update process before the last changes have been made.