My Saved folder is over twice the size of the rest of the project. I was just wondering if I can delete its contents and then have it start building up content again without it causing issues?
It is safe to delete. Your editor settings will go back to defaults, and project related data will be recreated automatically as needed.
You could of course make a copy of your entire project folder first, just to be safe, then delete that once you’ve verified that there were no problems. Technically speaking, there shouldn’t be any problems at all.