It's hard to say anything other than it should work, and I tested this recently and it worked fine for me. One common mistake is to extract the files on Windows and recompress them before deploying to macOS or Linux, which removes executable file permissions and will break your export. You need to extract the zip on the target system for it to preserve file permissions (the one exception being the Steam Devkit client). See this guide for more details.
Thanks for the response, I do extract the downloaded zip file after it exports, which seems to be the only way it can be uploaded. I tried to upload the zip directly with the steampipe and the web upload, but it always fails that way. If I extract first then upload with steampipe the game works fine on steamdeck, just not the achievements. Do I need a linux computer just to extract and upload for steamdeck? Or is there another way?