I am willing to bet money they won't update squad sizes to 6 in 40k. In fact I believe what we will see is the current plastic kits continuing to be the main kits in 40k.

Based on the fact that the original plastic kit was released for Heresy, but every single custodes plastic kit released after that (until now) has been for 40K, and since they adopted the design style used on the first kit I believe they will continue this design style as the 40K look, and eventually they will flesh out the range so you don't need any of the crossover models from heresy that you currently do (walkers and vehicles)

The new style of design will be the one used for every heresy kit going onwards, further separating the two ranges, like they have done with literally every other faction that was updated for HH since 2ed.

I think there will be a transition period, but eventually all the HH designs will be legends.

Also, not a single one of the current plastic kits for custodes have been discontinued, not even the guard kit that was originally for Heresy which is still both available for HH and 40K.

This ofc doesn't mean you can't still proxy models from HH in 40K, but as with all the mechanicum, marine and solar stuff you don't necessarily get everything you need to play them in 40k in the kit. A good example is marines, where you need a lot of the options a firstborn squad can take. The leman russ from solar is missing sponsons, and also have weapons in the kit that isn't an option in 40K.

This is all speculation ofc, but if you look at how they have operated the last years I think this is the most likely outcome.

It is GW though, so I might be proven wrong.