The spay procedure does not alter a dog's energy or metabolic rate. This has been studied effectively in our industry, and repeated studies have concluded that metabolism and energy remain the same following spay. In Bonny's case, I would look toward diseases that cause weakness. You have already ruled out a common disease that causes weakness, hypothyroidism, but there are others that would not necessarily show up in the blood work.
Addisons disease is a disease where the adrenal glands begin to fail and lack the ability to produce enough of the hormone, cortisol. Cortisol is integral in the sympathetic nervous system, the part of the CNS that enables the dog to exert herself, among many important functions. A blood test called an ACTH stimulation test can easily rule it or rule out Addisons Disease. It is quite treatable.
Another possibility is atrioventricular block in the heart. There is a structure called the atrioventricular or AV node that conducts the electrical pulse of the heart from its upper chambers to its lower chambers, enabling the rhythmic heartbeat. Blockage of this node due to physiological disturbances within the node can lead to dropped heart beats and commonly result in exercise intolerance. AV block is more common in herding breeds than in other breeds, so I would advise investigating this. A simple electrical evaluation of the electrical heart pulse, called an EKG would evaluate Bonny's possibility of AV block.
I see you are offline, so I will be exiting this chat. Please feel free to print out my posts for discussion with your veterinarian. Something is clearly wrong, as a 3 1/2 year old border collie should not be getting tuckered out. Best of luck to you and thank you for using Just Answer. Please let me know if I may be of any further assistance.