The core of the retooling issue in regards to the long-term is: who is retooling? If extremely senior people are getting out of the industry, it's probably a net loss to the chemical enterprise, but they're more likely to remain somewhat connected to the industry via consulting, etc. If large groups of chemists that have been in the industry for 5 to 15 years begin leaving the industry and "retooling", I believe that this would be a very serious issue, in that their experience, leadership and potential positive changes they would have made to the industry would be lost.The analogy I would make is this: back in 2006 or so, there were a spate of articles about the mid-rank officers who were leaving the military. For example, Maj. John Nagl was considered one of the US Army's leading thinkers on counterinsurgency theory; he left in 2008 (?). Now that he's employed by CNAS, he's not exerting his influence directly on the military. That's a net loss for the future, I'd think. If he were to retool and move out of the policy sphere completely, that loss would be even greater.
There's probably a break-even point for investment in a pharmaceutical labor pool; I'm going to guess that it takes at least 5 years to train a medicinal chemist to the point that they're at the top of their career potential. If you're shuttering sites and laying people off, some of those people and some of the potential long-term gain to pharma will be lost for good. While some of the more talented scientists would probably be picked up, some other talented people will decide "pharma is not for me" and leave. If the job market for medicinal chemists does not recover, the loss will likely be permanent.
What percentage of these mid-career scientists can pharma lose before there are real, negative long-term consequences to the industry? Lame to say, but we're about to find out.