Make sure you are up-to-date with the latest Sequoia, at the time of this post; it is 15.2 (24C101).
I have an M1 Mac Mini and the Focusrite Scarlett 2i2 3rd Gen and I've not had the problem where I had to reconnect the USB-C cable on the Focusrite after cold booting or rebooting the M1 Mac Mini on Sequoia. However, I am using the USB-C -> USB Type A cable to the Mac.
While you wait for Focusrite to address the issue, check if you are using the USB-C -> USB-C cable. If so, try swapping it for a USB-C -> USB-A cable connecting the USB Type-A connector to your Mac.
On the new M4 Mac Mini you do not have USB-A ports. However, the two front USB-C ports ARE NOT THUNDERBOLT like the ones on the back. The two front USB-C ports are USB 3.1 Gen 2 due to the rated speed being 10Gb/s while Thunderbolt 4 is 40Gb/s and Thunderbolt 5 (M4 Pro Mini) is 120Gb/s on the rear USB-C ports.
The Focusrite Scarlett line-up doesn't use Thunderbolt, it transmits and receives a digital audio signal at USB 1.1 - 2.0 speeds. The only time Focusrite products need Thunderbolt is in their studio rack mounted products with many more inputs. Due to the complexity of Thunderbolt, try plugging the USB-C to USB-C cable to the front of your M4 Mac Mini instead of the back.
USB-C is a complex technology, using a plain USB-A port greatly simplifies things or a USB-C using USB 3.1 Gen 2. On a PC, it would be a USB Type-A connector colored red. Some PCs only provide USB-C using USB 3.1 Gen 2 or USB 3.2 at best. Some PC's have full Thunderbolt 4 / USB4.
At the same time keep an eye out for Focusrite's potential fix and keep macOS updated with any new dot releases as they become available.