WordPress theme content upload issues

I created my own theme in artisteer, with content included. 66 pages and probably around 800 images. Each week my inventory changes so i make those changes locally in artisteer, then upload the new theme ridgewoodXX and then upzip it. in the dashboard i’ll change the theme to the new one and choose “replace Existing” as choosing “add new” wipes the whole thing out. It seems to work ok, the new content updates appears as i’ve built them locally in artisteer. The problem is it’s choosing to overwrite some of the media files with new ones of the same name. this is creating duplicate media content, and each week when i do that it gets worse. In some cases the same media file exists 10 or more times. IF i delete everything first as far as the pages and media in running theme and upload the new theme, add new etc.. then the sitemap changes because all the media ID’s are different. So it’s either massive 404s, or hundreds of duplicate content. Either way, i pay for it in my rankings. I’m not sure what if anything i can do to correct this so i thought i would reach out and see if anyone has any ideas