missing HDD after cloning main drive

Have you tried using disk management and allocating the drive? Hard to believe the drive would not already be detected and allocated since it was a formatted and working drive (I assume it was formatted). That would be ControlPanel/AdministrativeTools/ComputerManagement/DiskManagement.

Not seeing a drive has to do with F6 mass storage Drivers and how the "not seen" drive is set aka AHCI vs ATA vs IRRT.  MBR vs UEFI GPT is the other issue.

The 7010 in particular DOES NOT SUPPORT Secure Boot GPT and DOES Support Booting MBR XP.  UEFI PCI-E booting is NEVER AN OPTION with this model.  32 Bit XP and Secure Boot Windows 8 and 10 are not compatible with each other.

https://www.dell.com/support/driver/us/en/04/driversdetails?driverid=k0ck5

This will show up as STOP 7B inaccessible boot device.

"A required CD/DVD drive device driver is missing." error

And or when doing clean install one or more of the following errors.

Windows Cannot Be Installed to This Disk. The Selected Disk Is of the GPT Partition Style.

Windows Cannot Be Installed to This disk. The Selected Disk Has an MBR Partition Table.

Windows Cannot Be Installed on Dynamic Disk.

Windows Cannot Be Installed to This Disk. This Computer's Hardware May not Support Booting to This Disk.

Windows Cannot Be Installed to This Disk. The Disk May Fail Soon.

Windows Cannot Be Installed to This Hard Disk Space, Windows Must Be Installed to a Partition Formatted in NTFS.

no cloning nor migration apps stated nor revision !

cloning corruption has only one result, same thing,

no brand and model SSD stated, some are junk or must be SSD firmware upgraded. (not X300s drives)

not withstanding intels RST driver blunder on W10 , no OS stated by you, at all , just the word clone,

w10, 64bit version v1903 is the correct answer. (have it i do on d945G P4 HT,631 CPU  here' mad science lab...)

we can not guess OS here. sorry.

not stating DISKMANAGER Can not see the old drive, that matters most and not stated.

the OS Boots ok  on SSD , so what I do is put the HDD old in any drive dock or chassis USB

and erase it.

did you know that windows installer, Setup.exe can not see many things,?  as does not windows actual.

It does not like 2 things, alien drives (non MS formats)

and does not like 2 active bootable OS at the same time. if you used real migration tools (minitools) it asks you

do you want the old DRIVE out or  IN, after,  pick out. (if not it must fiddle the active partitions on the old hdd, to make it dead for booting) ok?

just erase the old hdd, and then Disk manager can use it , in a sata port.

I use  dock to do that and NEVER FAILS. to repurpose any hDD.

if the RST driver is bad (F6 tricks) did you know at intel they have  fix for that? there blunder, the driver they had did not work on all versions of w10  (count at 8 now) blunder.

here are all RST drivers,

I use killdisk.exe free (and safe) to erase all old drives, clean and single pass of 00s. no , paranoia just erase it.

then use it. This works best of all.

but so does the (allow old drive to work, in minitools (free) migrate drive)

what I do in most cases is run the SSD 0 only for 30days. if stable

erase the old disk and reuse it, ( data backed up first as always forever.)

btw I tested my cloning app on all dells here, everyone, and not one failed even the relic 380 !(2009)

it even works on my intel D945G mobo,  2004 MADE, W10 64RUNS HERE. A PENTIUM 4,  HAVE PROOF.

even my old AMD X2 64 runs w10-64 here(and all CORE 2 DUO and quads) stepping newest. (lab tests)

here are some cloning tips (migration)

old HDD. Back up data first. ( the endless mantra)

1: clean it first. get it 100% clean, CCLeaner then Defrag it as list step. 

If HDD is full of silly useless now videos , delete those next. (4 GB each, omg)

If w10 now do a inline update of w10 to w10 so no corruption !. (if this fails the HDD is BAD)

run full S.M.A.R.T test on old HDD if not Green but is red or yellow failed, it is NO GOOD> end story HDD.
"free crystaldiskinfo.exe"

2: then shrink the old HDD partitions, to less than new SSD size, tad less. (cuts risk this next)

3: run minitools appl free, (it can do #2 above super easy)

4: then migrate the hdd and tell it old drive will be removed, and park it for 30 days that hdd

5: remove the old HDD and park it off line on shelf, then when 100% sure the OS is not  corrupted, you then erase that old HDD, using Killdisk, I have  $15 HDD docking box, USB, (have many I do) and erase the drive using killdisk or if disk manger sees it delete volume.

6: then with DISK in SATA port, and disk manager running, format the drive and assign a driver letter first.

that is it,  doing clones since w95, 1000s done, done maybe 20 this year, retired, for me and friends /neighbors and family. (all are w10 no need to use any older OS ) not now.

on any old PC do not use UEFI, any of that. period. let the w10 installer do all steps for you , formatting erased drive to start. let it. (here is clone page with pitfalls covered)

the HDD has this UUID serial code, having 2 UUIDs same on one PC is not allowed, for sure on SATA ports.

use a docking station and erase the old HDD on any PC you have, easy as pie.

this is why I asked you what cloning tool you used,  due to the tricky handling of UUIDs.

All the IRST drivers are no longer available.

NVME PCI-E F6 drivers are NOT optional.

Note The IOCTL_SCSI_MINIPORT_FIRMWARE control code is not implemented in Windows 7 SP1 or Windows Server 2008 R2 SP1. Therefore, you cannot update the firmware on NVME devices that are running these operating systems. The control code was made available starting from Windows 8.1.

https://www.intel.com/content/dam/support/us/en/documents/memory-and-storage/Intel_SSD_6_SeriesInstallGuide.pdf

Windows PE F6 drivers are available as a cab file that must be extracted.  I use 7zip to extract the files to the root of my USB Flash Drive.  They also are placed in the my documents library for all users.

https://www.7-zip.org/download.html

https://www.dell.com/support/home/us/en/04/drivers/driversdetails?driverid=942xj

https://downloads.dell.com/FOLDER04120408M/1/WinPE10.0-Drivers-A04-942XJ.CAB

OLD Chipsets CANNOT USE current windows 10 AHCI driver or Version 17

9.6.0.1014 and 10.1.0.1008 and 11.3 were removed from download Sept 13, 2019 forever.

Version: 17.7.0.1006 (Latest) Date: 9/30/2019
https://downloadcenter.intel.com/download/29094/

Versions 9, 10, 11,  12  had many issues.

OLD Chipsets are Limited to 9.6 to 11.3

11.7.0.1013 is the oldest available.  This version DOES NOT support Old chipsets like the INTEL 945 950 960.  Those must use 9.6 to 10.1 or 11.3

Drives larger than 2TB REQUIRE 10.1.0.1008 or newer.

ALL VERSIONS Require DOTNET 2.0/3.5 and 4.7.2 or higher.  DOTNET is not installed by default in ANY version of windows from XP to Windows 10.

https://www.microsoft.com/en-in/download/details.aspx?id=25150

https://support.microsoft.com/en-us/help/4054530

Older Versions Still available.

Unfortunately anything that's plugged into that sata port is no longer showing (this doesn't appear to be a partition issue or hardware issue of the drive as I'm able to get the the HDDs to individually work on the other sata port).

As I say it's as if windows thinks a sata port is missing (but again the BIOS sees it)

I don't know if it could possibly be this simple, but here's what I would try:  Turn off that SATA port in BIOS and boot to Windows.  Restart, go to BIOS and turn that SATA port back on and boot to Windows.

How old is the CMOS battery, is it still good?

B keyed M2 drives are SATA so you would not be able to have B keyed drive and use SATA PORT 0 on the same motherboard at the same time.

unfortunately disabling and re-enabling the sata (1) port didn't seem to work, windows just doesn't seem to want sata port 1 to work

PS extra info

OS: windows 10

Cloning software: macrium reflect 

Dell model: optiplex 7010