Suppose you take two islands with one infantry.
You plot route to both - one after another.
Your unit disembarks at first island. Timing is 2 hours 15 minutes which is standard. It captures the island and goes to another one. Since it is your land, embarking should now take 42 minutes. But since you plotted route _before_ it became your land, disembark will take 2h15m again.
If you cancel order and plot route to second island once again, disembark will now take normal 42 minutes.
It is the same for all ports, cities included.
You plot route to both - one after another.
Your unit disembarks at first island. Timing is 2 hours 15 minutes which is standard. It captures the island and goes to another one. Since it is your land, embarking should now take 42 minutes. But since you plotted route _before_ it became your land, disembark will take 2h15m again.
If you cancel order and plot route to second island once again, disembark will now take normal 42 minutes.
It is the same for all ports, cities included.