You're lucky they were willing to do the exchange.I have a Tivo bolt that originally came with a 500 gb drive. I replaced it with a Toshiba 3TB model: MQ03ABB300. It worked fine hooked up to an antenna. After almost 4 years the unit started showing channels with pixilation. I had the extended warranty. I put the old drive back in and did an exchange. They sent me a new 500gb unit that worked.
You voided your warranty the moment you opened up the unit and the replacement of the drive is easily detectable by TiVo and likely some stats about the drive (e.g. model #, number of LBA blocks, drive serial number, etc.) are uploaded to TiVo as part of the logs. Such stats were visible in TiVo Series 1 logs when the backdoor code that let you access the logs worked.