Numbers file missing after permissions error / hard drive full

Have an 11-inch Mid-2011 MacBook Air (1.6ghz Intel Core i5, 4GB 1333MHZ DDR3 memory, 120GB hard drive) and experienced a strange problem with Numbers (v3.2) last night. I was working on a spreadsheet when I got an error that I didn't have permission to save the file. At the same time, I noticed a background notification that the startup disk was full. Thinking I probably just needed to free up some space, I quit out of Numbers (hadn't made many changes to the file yet), emptied the recycle bin, then tried to reopen the spreadsheet and found that it was gone. I have a link to it in my Dock, but that was now the question mark of a missing file. Looking for it by hand, it had disappeared from its previous directory and a spotlight search returned no results. In Numbers it doesn't even appear in the list of recent files anymore - it's like it never existed. I tried a restart (which has fixed some simple permissions issues for me before) but the file is still nowhere to be found.

I'm currently running a data recovery program (Stellar Phoenix), but seeing as that's going to take awhile to scan the hard drive, any other suggestions for what happened to it / ways to retrieve it? If the data recovery works, where should I even be looking? (I do have a backup but its a few months old, so finding a more recent version of the file would be VERY helpful).

Thanks in advance!