How should I use separate SSDs for Linux storage, and can I reinstall Windows later?

Applications are more complicated than personal files because their location depends on how they’re installed. Traditional packages usually put files in several system directories, while Flatpaks have their own storage location and can often be configured to use another drive. It’s usually best to keep core system packages on the Linux drive and put large libraries, games, media, and other data on the 2TB SSDs.

Reinstalling Windows later is generally straightforward: download the Windows 11 ISO or use Microsoft’s Media Creation Tool, create a bootable USB with that tool, Rufus, or Etcher, and install from it. Make sure you back up anything important first because selecting the wrong disk or partition can erase data.

Keeping personal data on another SSD is easy. You can format and mount that drive wherever you want, including as /home, so your user files are separate from the operating system. Alternatively, keep /home on the Linux drive and mount the storage SSD at a folder such as /mnt/storage. Just configure it to mount automatically at startup and keep backups.

Another option is running Windows in a virtual machine with something like VirtualBox or VMware if you only need it occasionally. That avoids reinstalling and repartitioning, although performance and hardware access may not be as good as a dedicated Windows installation.

Before removing Windows, check how activation is tied to the machine. If it originally came with Windows, the product key may be stored in the firmware. You can look for an MSDM table in Linux at /sys/firmware/acpi/tables/MSDM. You can also link the current Pro license to your Microsoft account. When reinstalling, use the same Windows edition so activation can restore properly. Keeping network, chipset, and storage drivers available is useful in case the fresh install cannot get online immediately.