Decide what you want Eve to be

Runeglaive is supposed to be an AP item. This is exquisitely clear from the fact that Sheen is actually better on AD previous to the upgrade to Runeglaive. Runeglaive has been touted as an Eve item time and time again. The vast majority of Eve's damage is AP. So why does her E do physical damage?

Eve cannot be built optimally hybrid, especially in a mobility meta. She can't stay close enough to AA regularly. Her primary source of damage has been, and will always be, her Q. Making her E deal physical damage is an artificial and construed way to make her deal less damage. You either need to build her sub-optimally (hybrid), or ignore that E deals physical and hope for the best (flat AP, no armor pen). Because of the nature of her abilities (where the cooldowns and AP ratios lie) AP Eve does more damage than hybrid Eve. So why is a physical damage E necessary?

Either acknowledge that you think E does too much damage, reduce the base damage and allow it to scale with magic pen, OR revoke the E to physical damage change, restoring Eve's identity as a real AP jungler, OR completely rework Eve. I get the feeling that the E to physical damage change was just to shove Eve out of any kind of competitive play due to there being no way to build her. If you don't like her with permastealth, or you think that is toxic, take that away. Give her something else. What's not pleasant is a champion with interesting mechanics being kneecapped by a damage type that makes no sense.

Given the rest of Eve's kit and identity, E should deal magic damage. Heck, if Eve came out today, she'd have some kind of magic damage on auto attack mechanic.