vite-istanbul/nyc only picks up untested files

Question

I am running Cypress component tests for a vue3+vite app. Instrumentation is done via vite-instanbul plugin. In cypress, I am able to get window.__ coverage__ and see the counters on different files. However, these files are never in the report. In the report, I only have the files that are not tested and thus get a report full of 0s.. Below is my config:

// cypress.config.ts

import { defineConfig } from 'cypress'

export default defineConfig({
  component: {
    specPattern: 'src/**/__tests__/**/*.{cy,spec}.{js,ts,jsx,tsx}',
    devServer: {
      framework: 'vue',
      bundler: 'vite'
    },
    video: false,
    screenshotOnRunFailure: false,
    setupNodeEvents(on, config) {
      require('@cypress/code-coverage/task')(on, config)
      return config
    }
  }
})

// vite.config.ts

return {
    plugins: [
      vue(),
      VueI18nPlugin({
        include: path.resolve(__dirname, './src/**/*'),
        globalSFCScope: true
      }),
      svgLoader({
        svgo: false
      }),
      istanbul()
    ],

// .nycrc

{
  "extends": "@istanbuljs/nyc-config-typescript",
  "all": true,
  "check-coverage": true,
  "reporter": ["text", "lcov", "cobertura"],
  "extension": [".ts", ".vue"]
}