Do you actually want advice, OP, or just validation of a decision you have already made? If you do want advice, you might be better off starting a thread with plans.
You have 3 issues:
Juggling the needs and feelings of 5 kids with a huge age range in a blended family without anyone feeling like there is favouritism. They are all at very different stages that are at conflict with their siblings needs when it comes to practical needs.
A house with an unusual, impractical layout that doesn’t suit your needs and makes it somewhat less desirable for a large property - 2 box rooms, a weird shape loft conversion with no bathroom, a downstairs bathroom, only 1 family bathroom on the 2 upper floors shared between 6 bedrooms (if you get rid of the en suite).
You are about to spend a lot of money on knocking down walls and new bathrooms that may devalue your property.
As you haven’t given us much to go on and we don’t know the layout, my suggestions to balance those things would be:
Go ahead with your plans but make the downstairs bathroom refurbishment really special and keep it for the 2 teenage girls to share eg a whirlpool bath, waterfall shower head, fancy make up storage, dimmable colour change lighting. Make it something more desirable than the en suite. Call it a spa room 😂
Leave things as they are. Move the 2 boys into the box rooms, the toddler into one of the medium bedrooms so she has her own play space, use the other medium room as a play space for the boys. Use the family room as a socialising/chill space for the older kids without toys. The boys are young enough that their own playroom is probably more appealing than a big bedroom of their own. Swap the toddler and your older son when he gets to secondary school and their needs have changed. If they know the future plan now, it won’t feel like you are taking something away.
Or as above but use the box rooms for the 2 youngest kids, the family room as a playroom so you can supervise, the upstairs medium bedroom as a chill/TV/gaming space for the older kids, if the 9YO is outgrowing toys already.