@Jan-Thijs I cannot guarantee that this will not happen. But I believe that cleaning the store is different than resetting the program settings. There is another button that can re-scan all Soundpools. But it will only re-scan the Soundpools in the default directories after you reset the program settings. I think a store cleaning should not reset the folders but only remove unfinished downloads.
I think you can also do this by hand by going into the folder C:\Users\YourWindowsUsername\Documents\MAGIX\Music Maker\ShopManager_mm31 and deleting all files from the download subfolder.