I've had this come up in at least three issues. Seems like the easiest fix is to make a backup of the existing file before any writes.

Update

I've closed this issue as it got to be a mess of multiple issues. The following two linked issues are where you should go from here:

• CONF-8898 - we should be able to recover from an automatic backup of confluence-cfg.xml if the main file is corrupted
• CONF-15549 - Windows servers will show warning messages about non-atomic updates of confluence-cfg.xml