EagleFiler doesn’t change the metadata of the files that you import. It sounds like this particular file was either:
- quarantined and manually overridden to open in a certain app
- quarantined and edited using a sandboxed app
- incorrectly marked as executable
Depending on the problem, it may help to select the file in EagleFiler and run this script.
There’s more information about the “unknown developer” error here. This error is sort of a macOS bug because document files don’t have developers—they do not contain code.