Hello for bumping this but i have the same question. That said, a dormant rootkit infection should still be detected, at least in most cases, by our standard malware scan engine, though I would still advise booting the other drive and running a Malwarebytes scan from there with rootkit scanning enabled just to be sure because certain rootkits, such as MBR infections/bootkits would still require our rootkit detection/remediation engine to be detected and removed/repaired properly.
Our rootkit scan works by detecting rootkit activity where we see what the raw data on the disk should be and compare it to what is being reported (by the rootkit, if one is active/installed). When a system is offline, for example on a secondary/slaved drive from another system, any rootkits which might be on the drive are not active/running and therefor are not hiding themselves. This is due to the way that rootkit detection works. Yes, if C: (of whatever the current drive is where the active/running Windows installation is installed) is not selected, then rootkit scanning cannot function.
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