I've only remastered once, and it was from screencapture source (what? this was Very First Vid, and I was young and stupid and thought it would be faster than ripping from the very same DVD, which mostly it wasn't). And I'm on a Mac. But for fiddly effects stuff I am increasingly inclined to take physical notes on what I am doing so that I can recreate things if I have to. Like, maybe someday I will be comfortable enough with traveling mattes to whip them out without the benefit of notes, but in the meantime I am writing down all the files involved and the parameters and stuff, just in case Current Vid Project has a HD meltdown and I have to start from scratch.

Good luck with remastering and with Shiny New Vid Projects!