I don't know about "picking a replacement", but if nothing else I think the UI should highlight if you are picking a redundant skill.
Very few classes get many skills, and proficiency bonuses are vital to success, so I think I would go so far as to have BG 3 completely prohibit you from taking a redundant skill. Since the Background is ONLY for two extra skills, the Background should be something you can change - or at least customize from the skills page.
The game should also, of course let you customize your background (within the limits of what the game's version of the background allows). This is important because some skills are available in multiple backgrounds, while others are found in no PHB background at all. (Three different backgrounds give proficiency in Athletics, but none give proficiency in Investigation or Nature.)
I really hope i could playing a Sailor Elf without loosing a Skill training
You're lucky in that the other proficiency is Athletics, so you've got some choice. For the moment, since there is no customization and no story attached to backgrounds, pick a different background. If you want to keep Athletics you can choose Soldier, and imagine that he was a soldier in the Navy. Or Outlander and get Survival as your second proficiency.
