Birthday Bonito evo erases Fantasy captain ICON chemistry

Buddy, this is not a bug. This is how evos works. Before putting your card into any evolution, please check the preview. It will clearly tell you if the card type remains the same or if it is changing. Some evolutions give you a new cosmetic card type and some don't. You need to use the appropriate evo chain to take advantage of the benefits.

For example, Birthday Bonito clearly highlight new card type at level 5. You should have checked evolution properly.
https://www.futbin.com/evolutions/649/birthday-bonito

If you are not sure, try to get help from external sites like FUTBIN or FUTGG. It is easy to build your evo chain and see how your card gets upgrades. In the evo chain below, you will notice the card type changes when the Birthday Bonito evo is applied at the end.

Hmm I guess you're right, however I think it's still weird that the chemistry is getting changed by just a cosmetic change. 

If that's the case, all the icons who're getting evo'd should lose their typical chemistry too because they're losing their icon cosmetic.

Icons don't lose their chemistry because they have a specific league and club. Normal players' chemistry depends on the card type i.e. rarity i.e. cosmetic.