My timeline pretty much depends on the breeding schedule. Since I don't have an 'official' business, I let them stay in longer than perhaps many others can... I don't remove them until they are four to five weeks old, sometimes even longer. I let it wait until they seem to be rather crowded.
The earliest I've ever removed them is when I've noticed that they are eating solid food.... Its easy to tell!
We used to turn the box up on it's side (secured w/wire so it would not fall) when they babies kept hopping out and about. This way they can still be in the 'nest' and yet out on the wire as well.
Boxes were made of wood with a wire bottom (used cardboard insert). These were nice, because as bunnies get older, can give more air flow (or not) by using or removing cardboard under nesting materials. (hay/fur)
An old fellow I met would also put a little 'lip' across the front of the box, inside, where the mom would jump in and out ..... This would help avoid babies on the wire, since they would sort of 'scrape off' when mommy would jump out.
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