Very odd, I would then have to guess the deletion of your file is then being done but another software/application.

I would first recommend to test the recycling bin in any of your arr apps by upgrading an existing release. The arr apps will move the old file into your bin on upgrade for you.

Then start by checking your paths. My guess is you may have your download application such as qbittorrent (qbt) posting your finished download directly into your media directory.

This would mean qbt downloads the file to the media folder, your arr app imports it to the same folder, then qbt deletes it after your seeding ratio finishes or after the arr apps finish import.