Hi!
How long has your boar been neutered? We strongly recommend a full 6 weeks post-op to make sure that there are not accidents, like the little baby in my avatar picture, whose dad is a supposedly safe over 5 weeks post-op boar (not one of mine). The recommendation also follows RSPCA (official UK animal welfare organisation) practice.
Neutered / De-sexed Boars And Neutering Operations: Myths And Facts
Boars, especially teenagers and young adults, when meeting other piggies of either gender can be swamped by theit hormones and lose access to their brain for a day or two. If it is getting too much for your sow and especially the baby, please separate and wait another day. Give them space on neutral ground without any hideys, but give your baby a place she can escape to, like a tiny tunnel or in a cardboard box with a little soft hay and two small exits on opposing sides that none of the bigger can get into. Ideally you give mother and baby 4-5 weeks to finish the weaning process naturally and allow the mother's body to recover a bit more and readjust to its normal hormonal balance.
3 weeks is the time when you need to remove boars so they cannot make babies with mothers and sisters and the gradual weaning process is generally fully underway, but not yet finished.
https://www.theguineapigforum.co.uk/threads/after-birth-and-baby-care.109389/
https://www.theguineapigforum.co.uk/threads/pregnancy-and-nursing-diet.109377/
Please take the time to read these guides here, including the information on boar bonding as well as group bonding and sow behaviour. You will hopefully find them helpful. Keep your boar next to mother and baby when sparated, so they can still interact.
If your mother is just running, but not fighting with him, it means that she is accepting him, so they will bond properly once he has calmed down.
Please be aware that babies are being put into place at the bottom of the hierarchy quite firmly even by their mothers once the weaning process has finished and the babies lose their protective status and are integrated into the group.
Bonding: Illustrated Dominance Behaviours And Dynamics
Sow Behaviour
When Sows Experience A Strong Season (videos)
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