I know that the newer Mac's do not have firewire ports and I know that it was replaced by the Thunderbolt port.

You claim that Tech Support advised you to purchase a "Thunderbolt", which you did.
Question: From where did you purchase this "Thunderbolt"

Having received this "Thunderbolt", you must have noticed that one end was Male and the other Female.
I'm guessing that you "may" have even read the setup section of the manual before proceeding.

I just "know" that you read the application note "Using Grass Valley ADVC Products with FireWire 800" which explains how to use the device with a Firewire 800 connection.

Having acquired all this knowledge, you apparently jammed one end of something into somewhere on the ADVC box and continued to jam it until something broke.

Question: Where did you try to plug this "Thunderbolt"?

You say that you purchased 2 of these ADVC devices. Hopefully you did not attempt to repeat the connection procedure with the second one.

If what I wrote above is correct, or nearly so, and given that the device was not defective, why would you expect the company to replace the device under warranty?

The instruction to purchase a "Thunderbolt" was perfectly valid.
The damage was not caused by you following their instructions, rather it was caused by you NOT following their instructions.