Installing a new version of the app might not be a full uninstall-install.
However if your installation package contains empty/initial version of your data files, they will get overwritten.
should be enough for the empty variant.
A possible negative outcome could be that you get an Update Error instead (since you are overwriting an existing file, though it resides in your own private folder, and it was not installed by anyone actually).
In this case just install a marker file
and check for its existence when your application starts. If it exists, remove your config files, and also remove the marker file (so the config files will not be deleted on the second time).