The ICMySQL have a system to auto update if there is a new available version it will download the script and replace the necessary files, the config.js will be kipped and not will be replaced.
If you want to use the system you only have to enable these options in the config.js file: Config.CheckForUpdates and Config.AutoUpdate.
Make sure that the FXServer process has permission to create directories and rename directories by default you will not have any problem with this.
This is the list of the involved files in this feature to help any developer to understand how it works:
src/utils/Updater.js