Whens runes or items are so broken you need to rebalance champs
Then just fix the item or rune jax is a great example of this you take away spear of shojin and he no longer has perma leap strike and counter strike and hes no longer unkillable and has amazing stick .Then you have conquer which you are changing you take this away and he no longer gets the ability to punch through tank stats for free basically .
What mostly needs to be done is remove runes and items that completely change how a champ should function like aftershock on mages needs to be changed to a %armor and magic resistance rune with small base numbers like 20 flat with 35% bonus so its used to make tanks more tanky not make squishy champs 2x as tanky .
Then you have the runes like phase rush that cause issues in lanes where without the rune the champ just gets run down and crushed but with it they can perma kite make matters worse it has like 75% slow resistance meaning if your a melee champ who uses slows to close the gap your entire kit is countered by this rune so while in alot of cases its ok there are cases where it makes some mus unplayable .
Now if you notice you remove most these runes and a few item functions and alot of the op/meta champs become basically average level champs all the mids using aftershock .
But for the most part items and runes need to mostly avoid changing a champs playstyle and if they do somehow change that not nerf or buff the champ cause when the item or rune is changed then the champ is left in an unplayable state .