These are for advanced users, by default MCEBuddy doesn’t convert video it has already processed (based on filenames). For some users their recording software generates the same filename over and over again for some recordings, so this setting allows them (in conjunction with delete original) to convert the new recordings with the same filename. Similarly for converted videos, its’ used by advanced users to daisy chain the conversions. See this post for an explanation:
The reason they are in red is because they can cause your setup to go into endless loop of conversions because it bypasses some typical safety checks. So if you’re going to enable them double check that you don’t have any closed loops in your setup.