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But this is another example of where installing applications to another volume can be problematic, because assigning D to the SSD will require removing that assignment from the HDD first, and if you have applications installed on D that are actively running within Windows, then you won't be able to remove the drive letter. If that works, then you'll want to shuffle drive letters within Windows so that it knows that the SSD-hosted version should be D going forward. If that doesn't work, I guess you could try reconnecting that HDD and then cloning from the SSD back onto that HDD to recreate the data there, and then hope that Windows will assign that re-created partition its original D letter in order to get you back to normal. And the SSD being assigned D might then allow those applications to start, since Windows will now see them at the expected D-based path. But if the SSD is currently E because that was the next available letter when it was first set up, then it should switch to D when there's no other volume in front of it. That is likely to happen since the HDD's disappearance should cause the SSD to get "next-available" drive letter assignment unless you at some point manually assigned E to that SSD, in which case it will remember that. But given that you're now in this predicament, the first thing I would try doing is physically disconnecting the old HDD in the hopes that Windows will then auto-assign the new cloned partition located on the SSD as drive letter D. I generally don't advise installing applications onto physically separate disks for this exact reason, or at least only installing non-critical applications such as large games or something. If you only cloned the HDD rather than the SSD and formatting the partition caused Windows not to start, it sounds like you may have installed some boot-critical application onto that D drive. There's nothing on a partition itself that says "I should be drive letter X".

There's nothing you have to do to get Windows to treat the new disk like the old one except possibly assign it the same drive letter as the old one, but you can't do that outside of Windows because drive letter assignment is performed by the OS.