I think ironically it was other way around - they issued write in such way that due to quirk in genuine chip it was no-op but actually worked on the clone.
More specifically: many of FTDI's devices, including the FT232RL, can store configuration data in an EEPROM. EEPROMs are conventionally organized as an array of bytes, but FTDI devices always access the EEPROM 16 bits at a time. The FTDI devices include some commands to read/write the EEPROM. For convenience, these commands use an address counting in bytes, but the official drivers and tools only ever use even addresses (so that the EEPROM addresses accessed never go "across" fields).
The FT232RL is one of FTDI's parts which has an internal EEPROM. An implementation quirk means that any attempt to perform a EEPROM write on this part with an odd address will be ignored. (This quirk is specific to this one part -- most of FTDI's other parts will perform this operation as expected.) This fact was apparently not known by the developers of the FT232RL clone; it will perform the write.
FTDI released a driver update which would, upon detecting a FT232RL, attempt to write zeroes to several odd addresses near the locations used for the device's VID/PID (vendor ID and product ID). These writes were ignored by the genuine devices, but were interpreted by clones as writing zeroes to these fields. This caused the devices to fail to be recognized when next connected to a host.
What's funny is that, as far as documented functionality is concerned, the clones work perfectly. In some regards, they actually work better than the originals!
That's not quite right. The addresses are in 16-bit word units; there are no unaligned accesses or byte offsets. You can write to any 16-bit word on other FTDI chips. However, the FT232RL has a quirk where it expects you to write adjacent pairs of 16-bit words sequentially, and only commits the write on the second one. If you only write the first half (at an even word address), nothing happens.
Usually, when programming the EEPROM in these devices (e.g. with FTDI's tools or open source ones), you write the whole thing at once, so those pairs are always written sequentially and it works anyway. However, if you try to write to some words at even addresses without following up with the next one, the FT232RL misbehaves and ignores the write.
Specifically, what happened seems to be that the FT232RL uses an internal 32-bit EEPROM. So when you write to even addresses, those writes are staged to a buffer in anticipation that you will subsequently write to the next odd address. At that point all 32 bits are written. The bricking code only ever wrote to even addresses, which involved a preimage trick to keep the existing checksum valid, since the checksum is at an odd address they couldn't write to. Instead they calculate what the value for the word before the checksum should be to make the existing checksum valid, and write that instead. Genuine chips would just stage all these writes in a holding register and never get to commit them.
Basically, FTDI decided to use an internal 32-bit EEPROM macro when developing this chip, and came up with this hack to shoehorn it into the 16-bit protocol (in what is arguably a buggy way). The clones just implemented 16-bit writes properly, which is the same thing all other FTDI chips (with external 16-bit EEPROMs) do.
(Source: I'm the guy who first figured all this stuff out back when this happened, including reverse engineering the FTDI bricking code and writing an unbricker).
More specifically: many of FTDI's devices, including the FT232RL, can store configuration data in an EEPROM. EEPROMs are conventionally organized as an array of bytes, but FTDI devices always access the EEPROM 16 bits at a time. The FTDI devices include some commands to read/write the EEPROM. For convenience, these commands use an address counting in bytes, but the official drivers and tools only ever use even addresses (so that the EEPROM addresses accessed never go "across" fields).
The FT232RL is one of FTDI's parts which has an internal EEPROM. An implementation quirk means that any attempt to perform a EEPROM write on this part with an odd address will be ignored. (This quirk is specific to this one part -- most of FTDI's other parts will perform this operation as expected.) This fact was apparently not known by the developers of the FT232RL clone; it will perform the write.
FTDI released a driver update which would, upon detecting a FT232RL, attempt to write zeroes to several odd addresses near the locations used for the device's VID/PID (vendor ID and product ID). These writes were ignored by the genuine devices, but were interpreted by clones as writing zeroes to these fields. This caused the devices to fail to be recognized when next connected to a host.
What's funny is that, as far as documented functionality is concerned, the clones work perfectly. In some regards, they actually work better than the originals!