EDIT: I solved this. Turns out I had too many worlds; I deleted some and the problem went away.
I made a survival world (no creative, no god mode/invisibility, no admin warp, minimal admin scan), then I made a world for testing. After this, glitches started showing up.
First glitch: I rejoined the survival world, and I had starter items and appeared at the spawn. All blueprints were replaced with the 2 or 3 I made in the testing world, the faction I made in that testing world was present, and the survival world’s faction was removed. Luckily, all structures stayed and no items were lost (although some credits may have been), and I was able to fly a core into my Warp Gate to get back to my base and continue.
The glitches don’t stop there. Next, I made a new world and chose to not copy blueprints. But guess which blueprints were copied? ...The blueprints from the testing world, same ones that replaced my survival blueprints.
Today I logged into that new world, and I spawned into the sector that I was in when I last played my survival world, with the same inventory. (Now I need to warp back to my stuff - not a big inconvenience, but the number of glitches are annoying.)
Edit 1: new glitch in the chain. Created new world and chose the other new world (the one where I spawned in my survival sector - an empty one, since I never built there - and with my survival inventory, despite it not being my survival world) as the spot to get blueprints from. Got survival blueprint instead.