Hurlbut's force is entering the city location in Harper's Ferry, although it is not capturing the city nor the region although with Hurlbut's force containing the Washington Bde and the Harper's Ferry region being devoid of enemy units there should be no issue of Hurlbut's force capturing the region and the city.
Since Hurlbut's force does enter the city, but the city is not captured, Hurlbut's force is subsequently not displayed on the map at the beginning of the next turn's plot phase.
The issue I was writing about--and incidentally had already reported in the beta-testers forum--is something which only occurs with lone leaders deep in enemy territory which is disloyal to the leader's faction: Vanishing General Post#14
The situation in Harper's Ferry is different in that a stack with non-leader units is becoming invisible.
I broke-out turn 3 of the scenario you uploaded DrPostman and executed the turn without making any changes.
Situation: Harper's Ferry has 60% CS loyalty and 75% CS MC at the start of turn 3.
Hurlbut with the 2nd MD Potomac Home brigade of 2 volunteer regiments is in Frederick MD plotted to march into Harper's Ferry with the Enter Structure SO--which previously would actually do nothing because it formerly only worked for stacks to enter structures that stack's faction owned at the start of the turn1)
. The turn-plot says that Hurlbut's force will take 11 days to enter Harper's Ferry.
The Washington Bde, currently in Washington DC has the Move by Rail SO set and is plotted to 'intercept' Hurlbut's force on day 3 in Frederick MD. This means they will joint Hurlbut's force and continue at a part of Hurlbut's force.
After executing the turn the messages note that the Washington Bde arrives in Frederick on day 3 and join Hurlbut's force on day 4. On day 11 it is noted that Hurlbut's force arrives in Harper's Ferry.
At the end of the turn execution Hurlbut's cannot be seen in Harper's Ferry. Hurlbut is of course easily found in the 'List of Units' in the Harper's Ferry region. Clicking on the flag next to Hurlbut selects his stack, which is then becomes visible in Harper's Ferry and the icon on his Tab of the Stack Panel denotes that his stack is indeed inside the Harper's Ferry city location1)
Tool-Tip of the region shows that the Union has gained 10% MC and is now at 65%:
Tool-Tip of the city shows that the city is still CS controlled and besieged(!!), but it appears that the structures inside the city, the armory and depot, are Union controlled(!!).
Apparently it has changed that a force plotted to enter an enemy controlled region with a city location will without any enemy units will actually enter the city. Previously the stack would only enter the region.