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Please see the official X‑Plane Support page for help.
I am not from Laminar Research; just a flight simmer from downunder.What is your operating system? What format of X-Plane are you running; steam or the official original version from Laminar Research.
Steam is a 3rd party hybrid taking a commercial advantage of the development work carried out by Laminar Research. It is not the same product as that from Laminar and you cannot mix one with the other. Laminar does not sell steam and has no connection with that product.
On the basis that you are running a Laminar Research version on a windows based system your last paragraph comments strongly suggests to me you have not installed X-Plane on either the desktop or a dedicated directory or onto a dedicated drive but installed the software into another directory eg Program files(x86). If installed using one of these methods then deletion would be total and not leave files as you have suggested. Until you do expect problems.
If you are running steam then you should take your question to a steam forum. From what I have seen with steam it installs the software in a different manner to that if you are running the Laminar version.
This site is no longer being actively maintained.