Hi. The first period covered relates to the so-called Third English Civil War between the Royalist forces under Charles II and the Parliament under Cromwell. The Royalists were mainly Scottish. The deportation happened, in the main, on the ships John & Sara in 1651. The ships lists generally found on the web are copyright so please take care of the source you use. The inbound, settlement and subsequent children are covered under the relevant colony project under the US project. There is discussion and activity relating to "indentured servitude" vs slavery in those projects. The source and origin of the individuals is managed under Scottish Clans, under the individual Clan; such as Category: Clan MacBean.
The second period, 1685, might actually relate to the religious persecution of Protestant families in Scotland following the arrival of James VII as King in Feb 1685; he was Catholic. They were not really POW's. There were two ships, Henry & Francis, carrying "Coventers" families from Leith (Edinburgh) to New Jersey, arriving New Jersey in Dec 1685. Again the Ships Lists are copyright depending on source used. These families are managed under the US immigration.
There was a later deportation, after the Williamite Revolution ("The Glorious Revolution") but this occurred later, in 1689 and 1690 and these were mainly Irish Catholics, although Scottish Catholics are noticed amongst the lists.
Depending on your interest it might be resolvable through the application of a category, if you drop me a note I can raise the issue with the Categorisation project. If there is a need to rationalise and clean up individual profiles it might be optimal to assist the current relevant colony project team. I notice you have the Irish Roots badge but if you are looking to help the Clans then drop a note to Maria Maxwell or myself and we can place up the Scottish Clans.