mIRC does not access your backup files in any way after they have been created by the installer. If they have indeed been deleted, this means that another application has deleted your ini files, most likely anti-virus software. This is actually quite a common issue
and we have seen anti-virus software behave this way in the past, where valid files are misidentified as a virus/trojan and deleted. The only real solution to file loss issues like this is to make regular backups.