If your cocoa butter chips off like that, you may be using too much. While you may want full coverage and an opaque layer of color, so much cocoa butter that it forms a shell of its own can be too generous.
Or simply skip the paper towel step. Scrape the molds as well as you can while they're soft and fresh and don't obsess over perfectly clean. Unless you're molding with white, a few stray bits of color scraped back in the melting tank when you make the shells aren't going to matter.