Does Magikarp lose IV % when evolved?

Nope. That's not possible. You just got inaccurate IVs before evolving

Some times when you have a pokemon and iv check it there are several options so you may pick the wrong one and when you evolve it and maybe power it up it might make there only one iv option the right one so thats my theory

It is more difficult to accurately calculate IVs for Magikarp due to its low CP range.

My guess is that you are using a site that gives you the average IVs but are getting the true IV after evolving. The fact this seems to happen with Magikarp for you reinforces this theory since his IVs are very hard to determine until evolved. You need to use Pokegenie or something similar and actually enter the appraisal information for anything close to accuracy with a Karp.