The mIRC installer is not aware of the download folder and does not access or modify it during installation, whether you choose the full or the upgrade option during installation, so it will be left exactly as it is.
If your download folder was erased, the only reason I can think of is that you are using anti-virus/security software that incorrectly thought your mIRC installation was a trojan/virus and automatically deleted your download folder and possibly other files/folders in the mIRC folder without telling you. You might find them in the quarantine section of your anti-virus/security software, unless it deleted them completely.
