The second file has multiple HIP 39048 entries, the first not. When I import the first, no multiple systems showing up in TCE.
When I export it, the file doesn't have multiple entries of a system. So all is looking good here.
Do you created the route with the build-in Route Finder function or manually?
I used the Cartography > Explorations > Create Exploration feature. Long story: Never used the cartography panel before (not really an explorer), however I am trying to unlock an engineer and dumping a good chunk of exploration data would help open them up. I saw another comment on the wiki about downloading CSV files from Spansh, so I created my first road to riches run on Spansh (52 systems). I followed the wiki and created a new exploration route and started entering the first 5 or 6 systems. At this point, I thought this is crazy. I read the wiki again and saw that routes can be transferred between players, so I played around exporting and importing files. I took a look at the exported files and they all listed one system per line. I started manually changing the systems and importing. Sometimes it works, sometimes, like the example I gave, it didn't. As I was importing and exporting exploration routes, sometimes with the same name, sometimes different, maybe I messed up some of the database internals.