Applications for appearance patents are made by different softwares. Will it affect the application?

You can't. When applying for a design patent, if the product's shape, pattern or their combination and the combination of color, shape and pattern are innovative, you can apply for a design patent for the product's shape innovation separately and use different software to make it, and the application will not have any impact. The process of patent application is: preparation of application documents, acceptance by patent office, preliminary examination, publication, substantive examination and authorization.