The “Ignore Single Files” option can be used to hide files which are only available in one of the directories.
What remains is the set of files that exist on both sides, so the listing answers “what changed?” instead of “what is where?”. Use it when one side is expected to hold extra files — build output, logs or a newer release — and you only care about the files the two have in common.
The files are only hidden from the listing; nothing is deleted, and clearing the option brings them straight back.