With Arduino IDE 1.8.5, the spiffs uploader creates a file that only contains what is in the data folder, so the SPIFF file size is small if the data files are small, e.g. 40KB. With Arduino 1.8.12 (Windows 10 app), the file generated is the full size of the file system, e.g. 2MB. It takes much longer to upload. I suspect it will also overwrite whatever files were created/updated using the SPIFFS editor.
With Arduino IDE 1.8.5, the spiffs uploader creates a file that only contains what is in the data folder, so the SPIFF file size is small if the data files are small, e.g. 40KB. With Arduino 1.8.12 (Windows 10 app), the file generated is the full size of the file system, e.g. 2MB. It takes much longer to upload. I suspect it will also overwrite whatever files were created/updated using the SPIFFS editor.