Is it possible that we have a confusion here between the moodle filing system and the computer filing system.
I do not how you have lost the backup file but the actual file is accessible in the computer filing system in the moodledata folder. You can search for it by name and it will be called backup-<site name>-<string including date and time of backup>.zip. eg "backup-egglescliffe-20050127-0155.zip "
You can search for it in the unix command line using "find -name back*" from above your moodle data folder; If you run a window manager then use the window manager filing system or in Windows using explorer.
If you need to you can then Copy the backup to somewhere you know about.
You can then use moodle to put it (via upload file) somewhere where you know that it is in the moodle internal filing system and then restore it from there.
Or did I misunderstand your problem?