Part 1: Nature of Pain and Suffering
I have to disagree with the implied premise that pain is suffering. Rather, pain is merely a sensation, often accompanied by physical aversion (reflex) and physiological stress. Suffering, in contrast, relates to will and its lack of fulfillment.
The core confusion likely springs from correlation -- that is, in many cases pain happens along-side suffering. Events that bring pain often hinder fulfillment. Events that hinder fulfillment often come with pain or discomfort.
Before a person develops the reasoning to act in accord with life's needs, innate mechanisms must enable self-preservation. Pain, which belongs more broadly to discomfort, is one such mechanism. Pain can be viewed as an automatic physical aversion about a thing or state. Absent of cognitive inhibition, pain can be expected to produce an automatic pull-back from a stimulus.
In some cases, pleasure or attraction accompany pain. What may be happening is that an agent is attracted to one element or aspect while being repulsed by another. Still, more mature agents are prone to partake in wholly painful actions when the outcome is understood cognitively as desirable.
A person is driven foremost by will, with sensations of pain and pleasure acting as signals, or heuristic indicators, of fulfillment. Suffering comes from perceiving actual lack of fulfillment -- not the mere suggestion of failure hinted by pain or discomfort.
Part 2: Ethics of Pain and Suffering
The will of an agent is normally tied to its nature. In the proposed scenario of separating a brain -- or even a bare mind -- from its body, the result may be an unnatural state of affairs where the instincts of the brain are disjoint from the needs of the body. The body is now presumably a simulation machine, whose needs and nature are likely quite different from those of a human body. One might say the will of the machine differs from the will of the brain inside it. Depending on circumstances, one may suffer while the other thrives. If we assume that suffering is bad, we may have a no-win situation.
The root disharmony here is lack of compatible will, very similar to cases of disharmonious servitude, possibly slavery. Ethics in these cases comes down to agency. To be morally permissible, an ethical stance could have to permit subsumption of agency, perhaps by holding the will of the simulation machine as inherently truer.
One such argument might say that physical beings have truer will since damage to physical bodies cannot be so easily undone as merely reverting to prior snapshots. Moreover, copying bodies has been far more expensive than copying memories.
A more extreme position might say that all minds, simulated or otherwise, are subservient to their bodies or genes or programming. From this perspective, one might say suffering of the inner brain is actually from ignorance of its role in something greater. Were it to learn and accept its place, it might cease to suffer, despite sensations of pain.
The proposed question is essentially one of digital slavery. The answer of ethics lies in agency; that of suffering, in identity.