Question Clean installing Windows 10 tomorrow, and have some questions

[Xenomenal]

Hey there!

New motherboard is coming in tomorrow after I had a tough time with MSI RMA and got a board refunded after weeks of troubleshooting. I stupidly had both an M.2 SSD and a HDD when I installed Windows on my PC 5 years ago. As a result, the Boot Manager is on the HDD, but Windows itself is on the SSD. If I clean install Windows 10 on a NEW SSD with only that SSD installed, what happens to the old Windows files on the other two drives? Can I delete them and be ready to go? Does the Boot Manager stick around on the HDD and cause issues? In other words, does a clean install solve the issue or will it just introduce more?

System specs for reference:
Windows 10 Home
ASUS B550-F Gaming
Ryzen 5 5600x
RTX 3080 FE
16 GB G.Skill TridentZ 3200MHz C14 RAM
3 TB Seagate Barracuda HDD (Boot Manager)
Samsung 960 EVO 500GB (OS)
Samsung 980 PRO 2TB (completely clean, want to clean install OS here)

Thanks in advance!

 

[Lafong]

If you clean install Win 10 on the SSD WITH ONLY THE SSD CONNECTED...

Then, when you reconnect the HDD, the HDD will be shown as D or E or whatever and you can then reformat it or delete all files or whatever you want.

The files on the HDD shouldn't matter at all.