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Are you sure you downloaded the Windows 11 ISO in the exact same language version as is set for the Windows 11 UI language in the Settings app in Settings - Time and Language - Language and Region, if the ISO is in a different language, that is the usual cause of not being able to keep your files and apps using the ISO for an in-place upgrade.
For example if you use the English language, if you downloaded the US-English version of the ISO, try downloading the International English ISO or vice-versa to see if you can keep your files and aps.
With regards to unplugging the drives, you cannot unplug the D drive, because it is just a partition on the same drive as the C drive is located on and even if the in-place upgrade indicates you cannot keep your files and apps, that usually only affects files stored on the C drive, but for safety sake, it may be best to copy any data on the D drive onto the E drive and disconnect that drive before performing the upgrade.