phillis grimble, I cannot comment from personal experience how these problems with security pass references are actually resolved. I can discuss the issues however from the experience of colleagues and friends.
When a pilot joins a new employer a request is sent out to the previous airline for a statement that they consider the individual fit to work airside. What seems to happen is that the airline simply fails to acknowledge the request. Chasing letters and 'phone calls are made to no avail. The pilot is then faced with explaining to his new employer that his previous Boss is inclined to be tricky when pilots leave. The issue here is pilot retention. This could be really tricky for an airline that is trying to expand rapidly for example. Equally the airline might be worried about poaching of pilots by a rival.
The pilots new employer might understand the local issues and find a way of resolving the problem, perhaps with other documentary evidence of employment. Equally the new employer might be concerned that the lack of a reference for the pass hides some other employment issue. Either way is a difficult and stressful issues for the pilot to live through.
Shut one door and another one slams in your face. What next.
I remember one Ops Director (now thankfully retired) who refused to supply a reference unless a form was provided by the new airline for him to fill in. He new full well that the airline in question did not supply 'forms' but simply asked for a letter of recommendation. Duplicitous behaviour to say the least. However, the Ops Director concerned was a known tricky character so the problem was easily overcome.
Obviously, it behoves the pilot to leave on the best possible terms. However . . . In an employers market these problems are more prevalent.
My view? A dreadful way to treat people. There is little to prevent it.
Hope you sort things out for your client.