Do migratory birds ever vary their routes in the event of some ecological/environmental change?
The answer is yes, they do so regularly. For example, here in the eastern USA, in some years southbound passerines (particularly Warblers, Flycatchers, Vireos, Tangers, Orioles and other small songbirds) in the fall travel south in vast numbers along the immediate coastline. Other years, they do so mostly down the Appalachian mountains or their foothills, well to the west of the coast and coastal birders have a very poor fall migration experience. This is believed to be in response to prevailing weather and wind patterns.
Another example: "fallout" in migratory stopover habitat. Background: most migrating songbirds do not like to cross large bodies of water in daylight or inclement weather. Daylight due to falcons, hawks, etc targeting them in the open with no shelter for escape. Inclement weather because of the downdrafts over bodies of water and because rain and wind can cause them to lose momentum/flight efficiency and they may have to put down in a hurry - which is impossible over a large body of water. So patches of good habitat (even small ones) directly bordering the large bodies of water are known as "migrant traps" - because they are an irresistible lure for migrants who have to put down in a hurry when approaching a large body of water and dawn breaks, there is bad weather, etc. When such habitat is destroyed, or created, the migratory birds either cease using it or begin using it, depending. At a large harbor or bay, vast lake, etc. - when such habitat appears or disappears, it can cause migrants to shift their routes and migratory stopover points anywhere from a few miles to a few dozen miles depending.
In terms of the Malta example, the sad fact is that many birds have no choice but to stop there. It's a survival tactic for tired and hungry birds crossing large expanses of the Mediterranean sea. Birds crossing large deserts also have no choice but to stop at oasis and any riparian corridors they may be able to find when they "run out of fuel".
And so if climate change caused a river to dry up and riparian habitat to disappear, birds crossing a given desert or dry scrubland would have to alter their route to find another stopover oasis, mountaintop, or riparian corridor.
With @Game Warden's specific example of the forest being cut and no longer hearing Cuckoos - that sounds like a migratory stopover location was destroyed/degraded and migratory Cuckoos had to stop over (or "fall out') elsewhere.
Loss of migratory stopover habitat is one of the biggest looming threats for migratory birds. To conserve migratory birds we obviously need to protect their breeding grounds and "wintering" (nonbreeding) grounds, but also need to preserve a chain of suitable migratory stopover habitat at regular intervals along their migratory routes.
* In terms of @Peter Connan's observation that he sees some kinds of birds migrating through his area in some years and not others - same over here. I have always thought it is a combination of two things: 1. The above example of variation in response to prevailing weather patterns 2. Here in years without much rain, we get fewer (or no) "fallout" events from migratory flocks encountering rain and deciding to set down in decent stopover habitat. When there is nothing but "blue skies and clear sailing" the thinking among birders here is that the birds tend to sail past without being forced to stop as often so birders don't see them as they fly over invisibly at great height. Many migratory songbird species (and some shorebird species) can and do fly continuously for multiple days without stopping or resting.
-- In terms of @Game Warden's question about whether migratory birds "learn to avoid areas where there is human interference" - I have not heard of such but that's not to say it doesn't take place. But if the human interference consists of destroying or degrading migratory stopover habitat, then yes the birds would be forced to look for suitable habitat elsewhere.
Edited by offshorebirder, 07 April 2016 - 07:18 PM.