Probably a secondary error caused by the program not setting up correctly with error here:
It might be because of a hash collision on the species name strings, but there aren't any duplicate strings/hashes. I find it odd that other linux users do not have the same issue as you...
I checked on my windows machine and not a single string has the hashcode listed ^. It would be helpful to know which strings are coming up as duplicate, if you're able to debug the program for that. You might also try installing the latest version of Wine (development) which is 9.13 (you currently have a stable release of 9.3).
And what technology does Bottles use? Wine. If Bottles uses an old version of Wine (not supporting .NET 8 compatibility) then you need to update the version of wine it uses, or use wine directly without Bottles.
This isn't an issue with PKHeX.
You've still not loaded a save file.
To export a save file, you must first load a save file. What would the program be able to export otherwise?
There are two concepts here. An individual Pokémon is not a save file; it is a pk* file. A save file is your entire saved data for a given game.
Did you forget to save your progress in-game before closing it?
If you are using an emulator, save states are not a replacement for saving via the in-game dialogue menu.
Berry Fix only adjusts the clock to be +365 days, outside of the bugged time region.
I can't recall if it's days elapsed since initial, or days elapsed since start (eg actual elapsed is 909-684), depending on when the initial time value was set.
Should be fine on the latest development build; this is caused by some Gen3 emulators appending RTC data to the end of the save file. The latest commits now properly handle this.