Have you actually heard what he played yet? It might be worth cooling the jets and taking on board how it all sounds as a final mix, which is the important thing. What might sound ok when it's just you and the guitarist might genuinely sound too busy when there are vocals, multi tracked guitars and all the rest of the padding are added in. I'd hold fire until I had time to see if I felt they were right. By your own account, songs were changed and you didn't nail some parts. If the guy has invested a lot of his own money and he's got a producer telling him this should change and that should change and you weren't available, you might have done the same thing in his situation. Like it or not, Metal is all about all about being tight and powerful. Sometimes non-standard basslines don't work in that context. If they've changed your parts, it doesn't sound like they've done it to spite you, it sounds like time was tight and the guitarist and producer had a vision they were working towards. The whole project sounds a little underprepared going into the studio. If you hadn't heard the vocals and your experience of the music was flling space with your bass in instrumental songs, then it sounds to me like there'd be a pretty good chance than things might get in the way of each other. If it really wasn't working, would you insist the song suffers so you get to keep a more interesting bassline?
I've produced demos for bands and had situations where guys were underprepared, didn't know the songs, didn't know their parts and some just couldn't play. I've never had a problem suggesting that someone else plays the right part to the requisite standard. If people are investing money into a recording then the final product needs to be as good as it can be to the end listener. Bear in mind, Pete Townshend didn't do much playing on Can't Explain. It happens.
As I said, listen to the finished product and see how it sounds. It really is all about the song as a whole, not the bass, not the guitar, the song. If you still feel the music is lacking then maybe it's not the right situation for you. If it sounds right when you hear the final mix, maybe you can take it on the chin and learn from the situation.