If by "fresh" you mean you need to reformat and/or overwrite the hard drive with a new installation from scratch (versus doing an upgrade in place), where all the programs must be reinstalled, then you definitely need to make sure you save off your last MC backup somewhere other than that computer. A thumb drive with sufficient capacity would do the trick.
The J River team may have other suggestions/instructions. FYI… I am not positive that MC backups capture the madVR settings, but I imagine it does. I don't know for sure, because I overwhelmingly use MC for audio only, so I have very little first-hand experience with madVR or JRVR's settings.
Good luck!