I recently ran into an error where upgrading SvelteKit via npm upgrade caused the following error:

Cannot find module './my-app/node_modules/@sveltejs/adapter-auto/adapters.js' imported from ./my-app/node_modules/@sveltejs/adapter-auto/index.js

What appears to have happened is the package.json file was modified and the following lines was removed:

"@sveltejs/adapter-auto": "next",

Adding this line to the devDependecies section and then rerunning npm upgrade or npm install seemed to fix it.

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{
    "devDependencies": {
        "@sveltejs/adapter-auto": "next",
    },
    "dependencies": {
        ...
    }
}

Update: This seemes to be resolved with the recent SvelteKit updates.