No. The existing files are left intact, but the domain is "pointed" at another directory containing the "parked" files.
They should be unaffected. Parking a domain just affects what shows up when you look at the domain in a web browser.
As long as you didn't change the "web directory" field when you created the domain, it should be in a folder with the same name as the subdomain, sitting "alongside" the folder containing the files for your existing domain. In an FTP client, if you start out looking at the files for your existing domain, you should be able to see the containing directory by pressing a "parent directory" button once from here. (The details may depend on what FTP program you're using.)
If you changed the value of the "web directory" field, the files for the subdomain will go in the location you specified.