It's not a problem, assuming you'll use the SSD to place the MSFS content there ( Community and Official ), when you are done and start the FSDT Installer, it will detect GSX to be not linked, so just click "Relink".
An IMPORTANT note, if your new SSD is internal, then it's all fine but, if it's external, be sure it's formatted in NTFS, because other filesystems like exFat or FAT32 most external drives ship with, do not support Symbolic Links.
