I have also been having this issue 🙁 It deletes my custom download template any time I update the plugin.
When WP updates plugins, it overwrites the entire folder. Including customised files.
To get around this, put the content templates in your theme folder instead https://github.com/mikejolley/download-monitor/wiki/Content-Templates#overrides
I am guessing that you have no control over this, but this does not make any sense. If I switch themes then I have to move my template. To me it makes no sense. I would rather see something that can be controlled in the plugin settings.
@chadsmiley I think it makes perfect sense to have “template” files in the theme. I wouldn’t think theme changing is a regular occurrence for most sites.