Yeah, I know. It doesn't have one. The more recent version does, but the old one doesn't. the Mod_info.json file lists it as 1.0, but I don't think it gets changed between versions.
I do change it between versions, and 1.0 should be the only version without a changelog, so it looks like the original version you were using was indeed 1.0. I do my best to make sure new versions are save compatible, but going from 1.0.0 to 1.3.11 is quite a leap, so I'm not surprised there was some trouble.
After looking at the code, it looks like the problem is caused by a reputation change being queued that later versions don't handle correctly, so sorry about that! I'll make sure this type of situation is handled more gracefully in the future.
For now, it should be possible to use new versions of starship legends if that reputation change is removed from the queue, which you can do by loading your game with starship legends 1.0 and waiting for all of the reputation change notifications to show up. Alternatively, you could set "removeAllDataAndFeatures" to true at the bottom of the options file, load up your game, save it, close starsector, and change the setting back to false. That should delete all starship legends data, including the problematic reputation change.
Again, sorry for the trouble, and thanks for bringing this issue to my attention. Let me know if there's anything else I can do to help.