Very Common Reinstall problem Not addressed in other threads very well

I have a custom Build PC. Selected the free upgrade to Win10 (currently my OS).
Situation:
I installed a 256 GB SSD for my OS, 4TB HDD (newer) and 1.5TB HDD (old left in for reference).
Tried to keep all OS software on SSD for quick boot up. The problem is that most software auto loads to the C: drive (SSD) unless redirected. Kids download gaming software all the time without redirecting to the D: (HDD). This download directing to the D: (HDD) was a problem that I'm not sure has ever been addressed, but when I installed the SSD it was a recognized difficulty.
Complications:
Built this PC for gaming and the kids. Nice to use when I get a chance (never, unless problems to solve).
The SSD has gotten stuffed with other stuff. The older HDD has failed (no problem, it just doesn't show up on windows explorer anymore). Windows 10 updates are installed on SSD and newer HDD. Machine went from boot up in 20 seconds, to 10 minutes now.
Question:
If I clean up the SSD and reinstall all the "Other" software on D: (HDD), can I do a clean Win10 install on just the SSD without wiping the D: (HDD)? Can I simply unplug the HDDs and do the re-install? What about licensing etc...
Will there be other complications? If the HDD is unplugged will it affect BIOS, or other important software related to the re-install? Should I be aware of other challenges when the HDD is replugged in? Are there any BIOS settings I need to do prior to unpugging/re-plugging it in? I plan on just removing the failed HDD in this process as well.
Comments:
I know of others in this predicament. All of them have installed SSDs for their OS and had this challenge. We don't want to lose our software or do a reinstall. I have anti-stuff malware defenses that include Betas and hard to get add-ons. Also have complex developer software that has gone up in cost to replace significantly.
In the re-install process can I change the SSD to D: and have BIOS see it as the boot disk (with the clean Win10 on it) and leave the HHD as C: for all else? will this affect future WIN10 updates? My guess is that the updates will try to go to C:.

Thanks for any and all assistance, comments and advice on this.

@R8to,

Have you thought about setting up a dual boot system? 1 completely separate OS installed for you, with only your account and login on it so the kids don't accidentally boot into yours and 1 completely separate OS installation for the kids? Use the SSD for your OS so you can control what gets stored on the SSD and what doesn't, and put the kids OS on the 4 TB hard drive.

NavyLCDR said:

@R8to,

Have you thought about setting up a dual boot system? 1 completely separate OS installed for you, with only your account and login on it so the kids don't accidentally boot into yours and 1 completely separate OS installation for the kids? Use the SSD for your OS so you can control what gets stored on the SSD and what doesn't, and put the kids OS on the 4 TB hard drive.

I guess, but would rather not. But if I did, I'd just get another SSD and load the OS there. Boot times are so short, I'd hate to go back to the HDD process. I don't use it enough to justify a dual boot, unless I was running Linus or something else on the other SSD.
Still this does not address how to Re-Install without damaging software on the PC. Any ideas? I'm not too smart, but have courage to get my hands dirty.

AddRAM said:

You always unplug all other hard drives when installing an OS

Windows 10 will auto activate after a clean install once you`re on line, just click skip when it asks for a key.

You windows drive is always C when you are booted into it, you can not and should not change it`s letter, and of course updates will go to C, that`s where they`re supposed to go.

All software should be installed on C, games of course can be installed on another drive, from C, that`s exactly what I do.

You say you don`t want to do a reinstall, then you say "In the reinstall process" what is it that you want to do ?

You do not change anything in the bios, you just reconnect your other drives after you reinstall Windows 10.

Make sure your W10 SSD is connected to the #1 sata port on the motherboard and make sure it is 1st in the boot order or 2nd if you want the dvd drive set as 1st.

After an install I always set my OS drive to 1st in the boot order and the DVD drive 2nd and then disable every other drive.

You can always boot from the dvd drive if you want to in the future by using the boot menu. (not the bios)

OK, I did not know this. All the posts talk about losing everything on the drives with a re-Install. So hence my reticence in doing a re-install.
So to summarize, you would move all unwanted software on the SSD to the HDD, then disconnect the HDD and do a clean, reformat, re-install on the SSD?
About the key, the PC did an auto install during the free period. I don't think I have a key.

R8to said:

About the key, the PC did an auto install during the free period. I don't think I have a key.

You don't need a key. Your PC already has a Digital Licence associated with its unique hardware ID recorded on Microsoft's activation servers. When asked for a key click 'I don't have one' and carry on with the install. Windows will check with the activation servers and activate automatically. Don't worry, the hard drive is not part on the hardware ID.

Just to be clear, I go to windows, select clean install. But my hard drive is disconnected with my browser on it?
How does that work? Assume I'm just stupid.

R8to said:

Just to be clear, I go to windows, select clean install. But my hard drive is disconnected with my browser on it?
How does that work? Assume I'm just stupid.

Download the ISO and create a boot install DVD using the media creation tool before you disconnect your other drives and boot from that to do the install.

Windows 10

Ok, after I figure out what you just told me, I'll let you know. Told you I was not so bright.
But in my defense I have an EE and CS degree from 1983, but have been a civil engineer since. Also AT in the uscg (out in 1980). So, I'm trying. I build gaming machines, but I'm lost on the software (acronyms included).

If your going to do a clean install on your SSD delete all partitions and do not format. then let the Windows installer create all necessary partitions. If I remember correctly when asked where to install Windows you select new and the installer will set it up with the correct directories.