Now, have you done a Spotlight search for the filename that you see when you right-click on the document? Once you can open it (in whatever app), you can Command-Click on the file's Name in the Title Bar and SEE the path where it lives.
I can see that the exported file did exist on my hard drive as it is on the 'open recent' list of my Preview App.
I have done a Spotlight search and no sign of the file. I've searched the bin, everything. It's really weird.
I must be doing something wrong during the export.. perhaps saving it 'in same file as original' is not a bullet proof way to save it.
It's quite a long edit so I'm keen not to have this happen a third time :)
In Onyx run almost everything in the Maintenance tab, deselecting things you may not want deleted, like Launch Services . Hit the "Options" button across from Internet and deselect more stuff like Cookies & Other Site Data, Browser History, Form Values, etc. (most of these are OFF by default). If you don’t know what something is, google it, or don’t run it, or ask me), then hit Run Tasks. After it's done it will ask for a reboot.
Also try to fix any directory damage by running Disk First Aid from Disk Utility: boot into Recovery Mode, (hold down Command-R when booting). When you're in Recovery Mode go to the Utilities menu and launch Disk Utility, say Repair Disk. When done go to Apple Menu for Startup disk and restart normally.
Also just doing a "Safe Boot" can clear out caches (restart, hold down shift until you see "Safe Boot" on the screen, let it fully boot, then reboot normally.