@ultrafine, yes totally possible to get back to 2.0.5. Just change the boards manager URL in arduino to http://update.wickeddevice.com/package_airqualityegg-2.0.5_index.json, select WildFire v3.2 from the Boards menu, and build and load the AQEV2FW_PM sketch. There's also a 2.0.6 release out there using package URL http://update.wickeddevice.com/package_airqualityegg-2.0.6_index.json if you want to try that instead of 2.0.5.
Regarding completely removing the old firmware, yes, it should have totally replaced the flash image aside from the bootloader. What happens is the Intel hex file gets side-loaded into an external flash memory, then the next time it restarts, the bootloader detects that image, validates it, and self-programs from it. The EEPROM configuration settings differ slightly from version to version, but I've been very careful to consider backward / forward compatibility issues with regard to that.
If you've got units that are getting stuck at Initializing CC3000, that's not good. I had seen such things happen sometimes and never got a 100% unambiguous root cause. I've seen CC3000's exhibit that behavior for a while and then mysteriously start working again. I've also seen situations where if I reapplied the patch programmer to update the firmware on the CC3000 itself, that could possibly fix it.
But honestly this is all bringing back bad PTSD memories for me. I think we'll both be happier if we can put those old WildFire v3 boards to rest in favor of WildFire v4s. I'll PM you and we'll work it out.