Dear JoonatanVahar,
I'm Dyari. Thanks for reaching out. I will be happy to assist you in this regard.
Sometimes the system installed on the SSD works fine with the new motherboard, however, most of the time it does not because of incompatibility driver issues. Therefore, you can have a try to see if your SSD works fine with the new motherboard or not, after that you can decide whether stay the windows as it is or perform a clean install.
If you can login into Windows, try the steps below to rescue your files:
https://answers.microsoft.com/en-us/windows/for...
For reactivating Windows after a hardware change, kindly check out the link below:
https://support.microsoft.com/en-us/windows/rea...
Please let me know if you need further assistance and keep me updated.