I'm going to take one last run at this, because it seems as though everyone wants to talk in circles about what they think. The short of it is that what you think doesn't matter.
I believe that FTDI did this with the intent of protecting their IP. I also believe it is a dick move to do so.
The facts are:
1) FTDI makes chips that are market standards when it comes to USB-serial conversions.
2) FTDI writes code for these chips, intending for them to function correctly using their code.
3) FTDI uses a chip foundry that they don't own, so "reverse engineering" chips is a distinct possibility.
4) FTDI cannot patent their IP, and they can't consider it a trade secret. As such, true reverse engineering is allowable.
5) Most reverse engineering companies (the kind where the term is liberally swapped with IP thieving) cut out expensive bits to make their hardware much cheaper, with less functionality.
6) In FTDI's case their firmware is cloned onto the "reverse engineered" parts, because the cheaper manufacturer doesn't want to spend money on developing firmware themselves.
7) FTDI released a new firmware that did not damage any of their products. While none of FTDI's products were bricked, the "reverse engineered" parts were.
8) Anyone who has such a bricked device can fix it with a little bit of technical skills.
9) Malicious intent cannot be proven on FTDI's part, because there is no way to legally do so. Even if they had malicious intent, the use of the pirated firmware in these "reverse engineered" parts constitutes a breach of the user agreements and an opportunity for FTDI to sue the manufacturer for IP theft and defamation.
Allow me to share a relevant story with you. My uncle buys an HVAC system for his house, from a bunch of contractors. They install it, and he calls up the HVAC unit manufacturer to activate the warranty. Low and behold, the unit was stolen from a new home (the contractors "install" it in the new house, report is stolen, receive an insurance check for the stolen property, and then resell it to someone else at a discounted price). What my uncle gets is the police coming over and ripping out the HVAC unit, which he paid for. The police tell him to file a civil suit against the installers, which will take from months to years to resolve. The criminal suit will be resolved well in advance of it, so the likelihood that there will ever be any reimbursement is almost zero. The consumer gets screwed, despite doing nothing wrong. The culpable party is a middle man, because the manufacturer did nothing wrong. Life is not fair, and this injustice proves it.
My knee-jerk reaction is to not like when the consumer gets screwed. At the same time, FTDI could either have made an innocent mistake or been protecting their IP/reputation. Either way, FTDI is completely free of culpability. No matter what you think/believe, the reality is that legally FTDI is free from sin. arguments to the contrary are easily answered with the question "can you prove it?" As nothing here can be proven to have the intent to damage their property, the proposition that FTDI is seriously in any trouble is laughable. Even the US's legal system has recognized that fast food isn't culpable for people getting fat. FTDI, likewise, isn't guilty for their firmware temporarily bricking cloned hardware illegally using their firmware for its operations.