Making a few assumptions here:
If you have Windows on your C: drive, and you clone the programs on your D: drive to E:, then all of the shortcuts on your C: drive will continue to point to D:
If you manually assign the drive letters for D: and E: such that they are E: and D;, your shortcuts will then point to the programs on the cloned drive. Hope that makes sense.
To re-assign drive letters in Windows 10, start Disk Management by right-clicking the Start button and selecting Disk Management.
Right-click the D: volume and assign it to F:
Right-click the E: volume and assign it to D:
Right-click the F: volume and assign it to E:
This swaps the drive letters of D: and E:, which I assume are your original and cloned drives containing your programs. You can then delete, clear, or even remove the E: drive since Windows shortcuts will be pointing to the correct volume (make sure to test those shortcuts first).