After a redesign of my website and a fresh new developing/staging setup I was also playing with the ubercart secure files directory for digital downloads. After I noticed this messed up my product/file download relationships I quickly restored the directory and it's file contents to exactly how it was before. All files related tables had been emptied by ubercart.
Then I noticed all users and product had lost their file downloads, so I restored the uc_files, uc_file_users, uc_file_products and uc_product_features database tables. This seemed to have fixed the problem but now all download links dont work anymore. On top of that, every time I try a download link or try to add files to a user all the aforementioned tables are emptied again!
Does anyone know why ubercart is behaving this way? is there any quick fix or hack to prevent this, even a temporary fix would do for now because I'll soon have hundreds of users complaining if I don't fix this.