What Does Restoring An iPhone Using iTunes Do Exactly?

I have a jailbroken iphone 4. Yesterday, I deleted a file from the system of the iPhone using iExplorer on Windows (I deleted the file so that I fix an issue), The issue I was having was gone after deleting the file from system.
The question: If I restore my iPhone using iTunes to factory settings, I know the jailbreak would go, but will the DELETED file reappear again?

Thanks for reading, now you can answer (if you know it) :D

It just means "make it like you just bought it". Wipes it clean and starts over.

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