"...does anyone know if when filemakerpro 5.5 opens up a working file it makes a temporary copy else where on the harddrive?"
That you can then find and open? Not as far as I know unless a script was specifically created in your file(s) to do that.
"...several of the active database files were reset to a blank template."
Two ways that I know of that could produce this effect: Save a copy with the (clone) option selected or Delete All Records from the records menu or in a script. Depending on how relationships have been defined, Deleting all records from one file can delete all related records from other files.
I realize this is a "benefit from hindsight comment" but, you should always make regular, at least daily, back ups of all your files to protect yourself from such mishaps.