Clockwork prosthetics and necrograft arms and legs are the rare examples of magic items to fully replace humanoid limbs, and unless they have a special ruleset on the matter they are as susceptible to antimagic fields or disjunction spells as any other magic item.
For any other magic item, it’s easy to predict what happens when they get affected by an effect that suppresses their magic : magic weapons revert to mundane masterwork weapons and other magic items stop having any effect and are totally useless. However, there are no rules about losing limbs except for some rules added by 3rd party publishers (that I tend to avoid except for a few rare exceptions) or I probably missed them, and the rules on prosthetics don’t explain what happens either.
If a magic prosthesis gets its magic suppressed does it :
totally stop working altogether and become inert (and apart from obvious penalties like not being able to wield weapons, how does it affect the wearer ?) ?
stop giving its specific benefit and still do its job as a limb replacement, imposing no additional penalty to the wearer ?