Having the same issue. Uploaded some 12GB of files to my OneDrive (migrated from Dropbox), gave it a month (if any indexing needed to be done), but still the Search Everything box stubbornly remains the most misleadingly named feature of OneDrive Online.
I can search by name for a file that I know with absolute certainty is in my OneDrive, and not have it pop up in the search results. I can even browse to the folder containing the file, scroll so that the file is visible in the UI, and search for its name;
still it doesn't show in the search results. Until it suddenly does, sometimes.
This is not a browser or caching issue. I keep Internet Explorer and Edge "clean" (use Chrome only), and the problem occurs in all browsers, also InPrivate/Incognito. It's like OneDrive doesn't index everything, or indexes horribly slowly.
Just now, I searched for a filename "Ordnerruggen", which is clearly visible in a folder in my OneDrive. The file wasn't returned. Then I made a screenshot of the issue to post to UserVoice, saved the screenshot to my Desktop (also synced with OneDrive),
and now the screenshot shows up as a search result (thanks to OCR, I suppose; the filename is visible in the screenshot). But the file itself still doesn't show up in the search results.
So OCR-ing a screenshot is near-instantaneous, but indexing filenames takes months? That's ridiculous!