How To Check an External Harddrive?

Long story short – A month ago, Hitman Pro detected something in S-1-5-21/something/Classes. The computer was then completely wiped and OS reinstalled. I switched to a brand new computer and used the old one to check for anything in my external haddrive i use for backups, Using Malware Bytes and Kaspersky on the drive itself, Then copying everything over to the pc so i could scan the files with ESET, Hitman Pro and Norton Power Eraser. Some emulators got flagged as either malware or suspicious (Don’t remember which as it’s over a week since that). Deleted some cracked software that i had for months or a year but that had never gotten flagged, Aside from Hitman Pro saying a .dll in Photoshop was potentially dangerous (Which only started happening a week or so before my pc was infected). I connected the hd to my new pc and searched again with MB and Kaspersky. Then the computer with everything mentioned. Nothing.

How can i make sure there really isn’t anything? I have no idea where the malware (Or whatever it was that got flagged) came from, And only Hitman Pro detected it.