What is the best place to update characteristics from?

Question

I am developing a real-time system which triggers an interrupt every few milliseconds. That data is collected in the interrupt. When a memory buffer is full, the data is then processed. 
 Currently they are 512 byte buffers. I eliminated the heap to free room. This is called on every interrupt to store the data. After the buffer is full, processing occurs (I know -- still in interrupt context) 
 array_y[array_counter] = y_sample;
	array_x[array_counter] = x_sample;
	array_counter++;
	array_counter &= array_bitmask; // wrap around @ 10 bit boundary
	
	if (array_counter == 0)
	{
 // Disable collecting of samples
 process_samples();
 // Enable collecting of samples
	}
 
 One thing leads to another 
 void process_samples()
{
...
 on_processing_complete();
...
}
 
 and another 
 
void on_processing_complete()
{
...
	if (m_callback != NULL)
 m_callback(...);
}
 
 
void hrCallbackFn(...)
{
...
	ble_hrs_heart_rate_measurement_send(&m_hrs, ...);
...
}
 
 And finally we work our way down to a call to the softdevice to do handle value notification, sd_ble_gatts_hvx. This hangs at a hard fault. I suspect the issue is calling this from within an interrupt context (bad pracice). 
 My question is: How/Where do I offload the signal processing to be in a 'main thread' priority as opposed to the interrupt context.
I am used to having freeRTOS or ucos to give me an event system. Please advise (operating systems are not a requirement for this project). 
 Is it sufficient to have a 'volatile' variable flag and process before the power_manage(); call in main()?

syntroniks · Accepted Answer

I seem to have solved my own problem in a hacky manner. I was originally using a priority 1 interrupt. Changing that to priority 3 no longer resulted in the hard fault upon softdevice call. Still interested in other ways of improving my code though.