You need to have all the changed files in a new themes folder. Otherwise they will be overwritten.

@Michael 🇺🇦 I had made a new folder, frio_custom even had in config to use frio_custom, but every time I do a git pull, it deletes frio_custom, so I upload a backup and try to set it as my theme, it only gives blank page, so I move them into the actual frio folder replacing all those files, and up looking at my instance, it only serves the new updates to frio, not my customization, other than the theme, where does Friendica call or store theme info? I have even tried to change from frio to frio_custom via config in db and still it fails, I was trying to keep my friendica instance current but I may have forget that if I cant get this theme issue worked out, should have been super easy, update place theme files back and done, but its not, at the moment I am working on downloading a full backup of site and db, to try and do it locally, and see what happens, going to be a day or so slow network

@Michael 🇺🇦 after updating with my custom theme all saved on its own, I still have no nav bar, no way to compose or anything

I know that some user reported the same after the last updates. For them it was enough to clear the browser cache. For you it could of course be that some files changed that you have touched as well.