I’m confused, it sounds like your saying that your Autosave vault has multiple capture scratch folders, each with a copy of the captured media that your working with. I don’t think that’s the case.
You should only have one copy of your captured media on the hard drive (not to a mention backup on a different hard drive). Is FCP’s capture location still in the default location? I always set my capture location to the root of a separate drive (RAID Array) dedicated to capturing.
The project files in Autosave Vault are just project files, they do not contain copies of capture files. Each version of a single FCP project file is referencing the same Capture Scratch files (the Capture Scratch folder is where your original Log and Capture or Log and Transferred footage “lives”). If you delete a file from Capture Scratch the media will go Offline in all projects that use it. So, NO! Don’t delete Capture Scratch unless you don’t ever want to see that footage again!
Of course your Capture Scratch Folder could be full of useless “practice” captures, old clips you don’t need or copies of the same files (I suspect you may have made) that aren’t actually in use in any project. You’ll have to decide what you do and don’t want to keep yourself (select a clip in Capture Scratch and hit spacebar to preview it), or get an external drive and copy some stuff off the internal drive to free space.
Open your current project, right click a clip in the browser (preferably one that is in use on the timeline) and choose “Reveal in Finder”. That will open the folder that contains at least one file that you do not want to delete. Take note of the location and repeat as necessary until you have a solid understanding of where all your media is stored. If you do have a few copies of the same capture files, notice whether your current project version “RP.5” uses the original “RP.1” captures or the “RP.5” ones.
If FCP crashes and some work has been lost I would reboot, reopen the project and go to File> restore project, choose the most recent one then save. Instead of going into Autosave Vault folder directly through Finder.