Are there any high ranking officers from this conflict that disappeared during or afterwards? Did any flee to America or other oversea colonies? What would happen with officers convicted of mistreating their soldiers during this time?
The lives and fates of most of the high-ranking Jacobite military officers are pretty well documented and fairly easy to follow. Some were captured, whereupon they were usually either banished from the realm or executed – like Simon Fraser of Lovat, Arthur Elphinstone of Balmerino, and William Boyd of Kilmarnock. Some escaped, often to France or elsewhere on the Continent. A few notable leaders (like Alexander Forbes of Pitsligo) hid in the vicinity of their homes and managed to elude capture for years after the rising had ended. Most of the most 'notorious' Jacobite leaders had their estates seized by the British government and their heritable titles nullified, or 'forfeited'. A few were pardoned and allowed to return (often to Scotland) years later, where some were able to reclaim their lands and, sometimes, their authority. Most did not, but they were nonetheless able to carry on with their lives amidst other pursuits, whether that be politics or mercantile endeavors in Britain or in the New World colonies. Simon Fraser the Younger, Master of Lovat, for example, went on to join the British army and perform admirably in North America in the French and Indian War.
A handful of the top officers within Charles Edward Stuart's war council subsequently wrote memoirs, and we therefore have some interesting depictions of post-rising life from the ones who survived. Amongst these, you will find published works by David Wemyss (Lord Elcho), John O'Sullivan, and John Murray of Broughton, as well as compilations of papers written by Pitsligo, Simon Fraser of Lovat, Lord George Murray, and others. Most are rather biased or infused with blame-deferral, but they are nonetheless essential reads for students of late Jacobitism.
As for the officers who represented ranks below the public leaders of the affair, their fates are a bit harder to trace. Despite the popular depiction of widespread execution after the Jacobite trials had been completed, only around 120 people were publicly killed by the government as punishment for treason, many of these being officers. Considering at the very least around 3500 prisoners taken (both military and civilian) during the rising out of an estimated 12,000-14,000 soldiers in total, the execution rates were very low indeed. Figure around 37% of prisoners during the rising were sentenced at all, with less than 10% of those being executed – the vast majority of those sentenced were instead transported to the colonies to serve terms of indenture. Most Jacobite prisoners, however, were released without trial or sentence through bail, pardon, or simple discharge.
Despite the government's focus on attempting to capture as many officers involved in the rising as possible, I am convinced that plenty managed to evade capture and return to their homes. This was clearly one of the primary motives for the British army's subsequent cantonments in Scotland and the brutal campaign of suppression that followed after Culloden. After three major and two minor Jacobite-related events in the span of a hundred years, the British government was not going to let it happen yet again.
Shifting gears to the recruitment process and the 'mistreatment' of Jacobite soldiers, this requires a more complex response than I can offer here. In fact, my own work heavily focuses on the motivations of the common Jacobite soldiers, as well as the tactics used to recruit them into the army. My doctoral thesis offers quite a bit of space and analysis of this very question, so I might refer you to download it for free and have a look through at your leisure. Within it you will also find more information about the judicial process surrounding Jacobite trials and further examination of the Jacobite army's rank-and-file constituency – as well as the differences in structures of prosecution between plebeians and landed gentry (including officers), which might fill in some of the gaps above.
I would also point you to the following short reading list, which contains a handful of titles that will most certainly fortify your background knowledge about the questions you have raised here. I would consider all of them essential for that purpose, and from there the sky is the limit.
Hoping this has been of some small help!
With best wishes,
Dr Darren S. Layne
Creator and Curator, The Jacobite Database of 1745
(recently of the Institute for Scottish Historical Research, University of St Andrews)
Before I respond, could you please clarify which military leaders you are asking after? This could be interpreted as an enquiry about British military officers or those from the Jacobite army. After I receive confirmation from you I will be happy to reply.