All 7 of them? I don't think they're going to be a problem. Whether or not the older fans complain about the Phlogiston being absorbed by the Astral Sea, I think that 5e Spelljammer will succeed on its own merits, not based on the feelings of the very few people that actually have been fans of it since it came out.
I think if it comes down to "Oh, in 5e spelljammer's lore, you can take a Squid Ship to a mining colony built on the petrified remains of a dead god" versus "oh, in 2e spelljammer's lore, if you tried to shoot a ship in the Phlogiston with a cannon, everyone on both ships would die" . . . the rule of cool would win out 9 times out of 10. I don't have anything inherently against the idea of the Phlogiston, I just think that being able to go to the Astral Sea and find the petrified bodies of dead gods is 100 times cooler than anything you could do in 2e's Phlogiston. And I think the bigger segment of 5e's newer players would agree with that, too.
In my opinion, whether 5e Spelljammer succeeds or fails will probably come down to the price, the new format of 3 small books, and the fact that it might be too wacky for some people (but, looking at Gen Z's sense of humor, I really don't think Spelljammer is going to be too wacky for younger D&D players).