Trying to make an Aereni High Elf. The Aereni just means I can replace the Elf Weapons Training trait of the High Elf with the "Aereni" trait which is:

An Aereni elf can choose one skill or tool proficiency. Your proficiency bonus is doubled for any ability check you make that uses this chosen proficiency.

This doesn't limit your choice to "new" skills or anything just to pick a proficiency. You should be free to pick one you have not yet got or one you do. Basically, you pick ANY skill or tool whether you're proficient or not and become an expert in it. That's the RAW and RAI of it.

So, making an Arcane Archer I wanted to choose Perception - sure I'm already proficient as an Elf, but this makes it Expert level and there is nothing stopping me from making this choice, by the rules because I am not limited to choosing "new" profiencies. This is perfectly valid by the rules but whenever I try the Character Builder keeps removing it and asks me to choose something else.

I can create a homebrew feat to make an ad-hoc fix but wanted to flag this up so it can be looked into.

I just tried it, and I was able to make an Aereni High Elf with expertise in perception using Aereni Elf Feature with no problem. 

Try refreshing the page, making sure there is nothing else giving expertise, then post link to builder if problem persists.

Nope. Everytime I choose perception then have to go pick something else like choosing a class, choosing a proficiency elsewhere (class, for example) or use any menu, it removes the proficiency. I've refreshed, doesn't change anything.

Builder link, char not yet finished: https://www.dndbeyond.com/profile/Cyb3rM1nd/characters/9129919/builder#/race/manage