Did you look at the FAQ document (that has even more details posted about that card)? One of the things included there is this:
If the check was triggered by Scottish Lords Rebel, the procedure is always the same:
1. If result is alliance with England or the Protestant and Mary Queen of Scots is alive in Scotland she becomes captured in England.
2. All Scottish spaces come under control of the power who wins the diplomacy roll.
3. All units in Scotland not allied with the controlling power are displaced. Units allied to the controlling power remain in place.
4. Remove all Scottish troops from the map and replace with 2 Scottish regulars in Edinburgh.
The English and Protestant units can remain in place since they are allied. But also don't forget Step 4 (adding 2 Scottish troops to Edinburgh).