So I initially didn't realize that levels wouldn't auto-publish upon saving, so when I discovered how to load from a backup, I was relieved. However, what I noticed is that 1 backup had my build mostly complete but the world had no base anymore, and every other time I loaded that same backup the base loaded but half my build was gone.

Will I need to make myself a new base (I made my latest save on-top of my build so I can move on-land), or will I need to make myself a new base?

Sometimes the saving level process messes up on a few parts. You'll need to make a new base manually if you want to load from that file.