Yes, it does this.
When you update the software, all files included with the software (the sample tournament, template files, etc) will be written to the install folder, overwriting the ones that are already there. If you choose to save over these files, you're going to lose your changes when you update the software. This has been noted on the Download page (
http://www.thetournamentdirector.net/download.html) since 2.0 was made available, or perhaps since the first update to 2.0 became available. So, you should really save your own versions with their own unique name, to ensure you don't lose your customizations when you update the software.
Now that the TD uses Data Stores, updating the software will only update the files in the TD's install folder. This doesn't do most people any good, as it is at least
recommended that you don't use the install folder as your data store. So each time you start up the software, the TD copies included files to the current data store (basically, it "inits" the current data store). This is the only way for updated included files to find their way to the data store folder for people to use.
Take a look at the "dataStore.txt" in the lib folder of the TD install folder. This file is the manifest of files that are copied during the data store init process. Changing it will affect what is copied during a data store init. So, you could either remove the files you don't want copied from that list, or create a script to delete the files each time. Of course, an update to the software will replace the dataStore.txt file.