As long as you save the SH3 folder created in the documents folder you can save your current career. Be sure to take careful note of what mods you have activated so that when you do the new install you can re-start from your last save point. If you activate new mods or leave some out it can cause numerous problems; most prominent one being CTD after loading the save game. My current career has survived 3 transfers now due to all the hardware swapping that's been done to this (and the previous one) current laptop.
Before wiping the disk I take not from JGSME what mods are enabled and their order. Re-enable them with the new install and you should be fine. There is also the appeal of a fresh install, and wanting to start a fresh new career.
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