Problems with material suppliers is nothing new, my guess is that LT's current material supplier is having problems with the purity and it is causing problems for the LTZ, this would not be a wafer level problem, given the higher performance level, impurities are critical. We've had problems with resistance alloy suppliers in the past, going back decades, which caused a lot of trouble. This happens and often finding a new supplier is the solution. Rest assured, there is no change to the LTZ as it is made, there is absolutely no move to put it in a different package, it wouldn't work to spec otherwise. I rather doubt it has anything to do with the die leads either, but exactly what is causing the problem is unknown outside of Linear Tech as such.
Back in the old days, we had vertical manufacturing, a semi house did everything, raw materials came in one door and the finished product came out another door, everything done under one roof in effect. Nobody has that kind of integration now, it has gotten too expensive and too many regulations. And with that change, managing quality control of materials became much more difficult, many books and articles have been written about the supply chain and how it is spread around the world complicating quality control. It is no simple matter these days.
This kind of disruption happens all the time in ICs, if you kept an eye on delivery dates, you can always tell when supply is not meeting demand for a myriad of reasons and raw materials are often at the head of the list. A lot of those raw materials comes from countries that are not the most stable on the planet. Those that process the raw materials are also scattered all over the globe, just try keeping control of all of the variables involved all the time. The fact is even highly reputable companies can run into problems and it can take a lot of time to fix it, customers can't wait very long in most instances.