Hmm yes, I'm still troubleshooting it. I had deliberately hidden the mobile friendly page from indexing, as I preferred the main domain to be the one listed in search results. So perhaps it was the combination of the injected code and that?
I also had that injected code on both the main home page and the mobile page, so that they redirected to each other depending on the users screen res. Perhaps those vice versa redirects caused the indexing issue?
For now I've removed both the injected code and the noindex tag on the mobile page, added a link to the mobile page within my site, and requested reindexing. We'll see if all the pages reappear.
Please let me know if you think the above were the likely causes, and if there's a way to keep the mobile page unlinked within my site, and not indexed, yet have my mobile and desktop pages redirect to one another based on screen size.
I'm nervous about search result visibility with testing now! But when I have time and perhaps a gap when I'm not concerned about search results, I'd like to get it working.