If you configure a mass action to export products based on a hourly cron trigger, and if you configured your cron task in the configuration, each hour, the system will generate a CSV automatically.
Now you could potentially manually trigger that cron URL from the command line.
But that's all I can propose from the command line for exports.
Regarding the import: Import is for inserting the initial data, not updating it. So yes, it replaces all the data and if you don't specify the options in the CSV, it will wipe them.
If you want to actually update products information, you should do it via the mass action import filter (the CSV should be the same).