Thanks for the replies. This is a better bottle, so there are some logistic challenges to cleaning it out (as opposed to a bucket).
The reason it spoiled was a good lesson learned for me. I made a harvest ale that I fermented in a glass carboy. Getting 5 gallons of wort in a glass carboy didn't work too well and I had to deal with the whole hops clogging up first my funnel and then my strainer. I am convinced that's where I lost it.
When I racked to secondary (another lesson learned for me with a harvest so that I don't lose so much beer with the hops at bottling), it didn't quite taste right. When I went to bottle, I knew it was lost.
My concern with the better bottle is whether it could have small abraisions from the past few years and whether those could harbor bacteria despite the best sanitization methods. I'm sure other folks are wondering if they had a bad batch if they should dump the carboy as well.
I am going to rack another whole hop recipe into the better bottle today (it doesn't smell bad) and I will post my results in a week in case anyone has this type of question again.
Thanks!