Files stored in Google Drive can “go missing” when they become “orphaned”. This is when the file exists but the parent folders it was located in are deleted.
For example, this can occur if you create a file in a folder owned by someone else and that folder is deleted. Your file isn't deleted along with the folder but it no longer has a parent folder.
To locate your orphaned files you can issue the following advanced search:
Or to speed up the process just click this link.
You can “re-home” files by selecting and dragging them to a folder in drive, or by right-clicking on a/some files and using the “Add to my drive” option.