The changes I made to Shizuya's character script to address some combat appearance issues, I also disabled her serialization (for saves) because I thought all her data was static for the most part. I ended up overlooking the stored location variable. The fix should restore her serialization again, but you may need to wait a while for her ship to respawn at a select location if it doesn't do it instantly. I'll need an affected save file to make sure though.