Riot, while you're having to re-implement a feature that already existed
Since you apparently have to redo the part of the client that remembers the last runepage you had selected, which doesn't make sense that you need to do that in the first place...
How about making the game remember the last runepage you selected for that particular champion after locking them in. It doesn't have to be perfect, I know the runepages are saved at #1-20, so just have the game remember the number for each champ.
I can't imagine this would take a lot of resources and you're already having to redo this part of the client, so if it's possible, why not do it? It won't solve every case of selecting the wrong runes but it would reduce the number of cases.