This topic came up in a recent Google Webmaster Central hangout when a site owner asked how Google deals with a site when part of the content is not usable on mobile.
The site owner asked if the content will be crawled, or if it should even be included in the mobile version at all.
In response, Mueller said Google’s systems will likely get confused by this type of site.
Google will not completely know if it should switch the site over to mobile-first indexing, and will probably choose not to in order to stay on the safe side.
Mueller suggests looking into ways of making it more obvious for Google to determine that a site is ready for mobile-first indexing.
That might include moving most of the problematic content over to a desktop-only version of the site, which Mueller said is perfectly fine.
Mueller’s full response can be seen in the video below, starting at the 42:47 mark.
“I think that’s something you have to think about yourself in the sense that you can always have some part of your pages be on a mobile version and some part not. That’s perfectly fine as well.
What I suspect will happen with regards to mobile-first indexing here is that our systems will be a bit confused, not completely know if they can switch the site over to mobile-first indexing.
For the moment we would probably stay on the safe side. So if you’re curious about mobile-first indexing, if you want to prepare your site for that, I might look into ways to making it easier for us to recognize that your site is ready for mobile-first indexing and that we can switch it over.
Which might be – you move your Flash games over to a different site or something like that to really make it clear for us that this site is ready for mobile-first indexing, and this other site here is not suitable at all for mobile-first indexing.”