A few weeks ago, I pulled some of an IPA I was making and force carbonated it so my friend and I could try some. While it was not the bitterest I have tasted, it was definitely an IPA. I bottled the next day. I tried a bottle last night after it's been in for about two weeks. I couldn't taste any hops at all. It was still a delicious beer, but it tasted a lot more like an amber than an IPA. What process could happen inside the bottle that could cause practically all the hop flavor in a beer to dissipate, and how could this be prevented in the future?
Hm. Hop flavor will degrade over time but usually it takes a few months or more, not a couple of weeks. Hop bitterness will degrade as well, but it takes much longer, with about 75% of bitterness intact after a year. That being said, I'm guessing there are other factors at play here, not just degradation.
What temperature did you try these beers at? Temp can greatly influence taste, and if the beer you pulled off was warm while the bottled beer was cold, it could seem like the bottled beer had less flavor. This is the only thing I can think of offhand, it might also be good to post you recipe so we can troubleshoot it better.
Here is a potential answer to your question:
My question is what temperature did you store the bottles? Isomerization of the alphas (the source of the hop bittering) is definitely the most likely culprit in this case. Hoppy beers in general need to be kept cold (well under 70F) to maintain the bite.