TypeScript d.ts file icon has an X

This icon means that the file is explicitly excluded from indexing.

Was it generated by the compiler?

No, aren't .d.ts files meant for declaring your interfaces? I use it like so:

Home.d.ts:

interface HomeProps {

   ...

}

Home.tsx:

class Home extends React.Component<HomeProps> {

    ...

}

Please check your .idea/workspace.xml - do you have "TypeScriptGeneratedFilesManager" component there with your d.ts listed among "exactExcludedFiles"?

<component name="TypeScriptGeneratedFilesManager">
    <option name="version" value="1" />
    <option name="exactExcludedFiles">
      <list>
        ...
      </list>
    </option>
  </component>