When copying a MIDI region, Ardour has to decide whether to make the copy refer to the same data as the original or not. If it does refer to the same data, then editing either the copy or the original will affect the both of them. If it refers to an independent copy of the data then each one can be edited without affecting the other.
Session > Properties > MIDI > MIDI region copies are independent can be used to control the default behaviour when making a copy of a MIDI region.
When enabled, every new copy of a MIDI region results in a copy being made of the MIDI data used by the region, and the new copy of the region will refer to that data.
When disabled, every new copy of a MIDI region will refer to the same MIDI data, and thus editing any copy will change the contents of all of them.
Changing the status of this option has no effect on the existing dependent/independent status of existing region copies.
Right clicking on the MIDI region to be independent then selecting MIDI > Unlink From Other Copies makes it independent: the copy is now using its own version of the data, and edits to the copy will affect only the copy. Other copies will continue to share data.
Note that the copied data only covers the extent of the region when the copy is made. If the region was already trimmed and then a copy is made, an independent copy will have no access to data that is earlier or later than the bounds of the region it was copied from. Put differently, making an independent copy of a trimmed MIDI region only retains the visible part of it.