I recently swapped out my motherboard and CPU, and I'm facing a weird issue with my setup. I have Windows installed on my SSD (C: drive), but when I disconnect my secondary HDD (D: drive), my system won't boot up at all. I thought Windows was supposed to boot from the SSD by itself, which has me confused. I suspect that during the installation, some critical boot files ended up on the HDD instead of the SSD. I'm hoping to get clarity on two things: why this is happening and how I can fix it so my SSD can boot solo without needing the HDD to be connected.
4 Answers
What likely happened is that when you installed Windows on the SSD, it detected the existing boot partition on the HDD, so it didn’t create a new one on the SSD. This is because there was already a valid boot partition available during installation.
Yes, the EFI partition, which is critical for booting, seems to have ended up on your HDD. During installation, the installer tends to default to writing the EFI partition on the drive with the lowest number, which isn’t always the intended drive. You might be able to rebuild the EFI partition on your SSD, but it can be tricky and sometimes doesn't work as expected, based on my experience.
It sounds like your boot partition might be on the HDD. Sometimes, when Windows installs, it creates necessary system partitions on the disk with the lowest number, which in your case could be your HDD. To check if this is the case, look at Disk Management in Windows to confirm where your boot files are stored. In the future, it's good practice to connect only the drive where you want to install Windows during setup to avoid this issue.
When you install Windows, it creates several necessary system partitions, including one for EFI that holds the boot loader. Sometimes, for reasons that remain unclear (thanks, Microsoft!), the installer ends up using the wrong disk for these partitions. To avoid this, it’s recommended to only connect the drive you want Windows on until installation is complete.

Is there a way to resolve this without reinstalling Windows? Maybe using a boot USB to repair?