In the Futurama season 3 episode "Luck of the Fryrish", we learn that Fry's brother Yancy had a kid named Philip, after his lost brother. However, in the movie Bender's Big Score, we see Fry travel back in time and return to his life for 12 years before being hunted down by Bender and freezing himself in his ex-girlfriend's cryotube. Doesn't this mean that the history of Fry's nephew didn't happen as we saw it in “Luck of the Fryrish” (so it's a retcon)?
One can assume we actually pick up the story a few cycles through the time travel process.
Fry has already returned as Lars and begun to woo Leela. But if you pay close attention, everything that happens could have happened without Lars' presence. This suggests the Lars is simply an anomaly up until this point.
Once the time sphere is discovered, there are many cycles of slightly altered history where sometimes there are more than one character and sometimes there is only one. The alternate history we see where the young Philip Fry, Yancy's son, answers the door is just one of these alternates.
Now that the setting is clear, here's what happens:
Fry moves into the attic of the Pizza place he works at, Mr Panucci's, and watches lame 20's century TV. He sees the Rare female toothed narwhal Leelu, and decides out of love for Leela, to try to take care of this creature. He works here for a few years before they decide to set her free. This is still before the younger Philip Fry is born. He then ditches his entire life to join a long-voyage to the north pole, and is gone for something like 5-10 years. Meanwhile, his brother misses him and doesn't even know if he'll ever see him again. So he does what he was prone to do anyway and name's the kid after his brother.
Nothing in The Luck of the Fryish needs to be altered, Just like nothing in Jurassic Bark needs to be altered. They just left out bits in both of those episodes to make you think one thing happened, when something else was happening.
It is worth noting that these were, in fact, not planned during the breaking of those episodes. It just was a happy accident that the nature of a 22 minute show leaves loads of time cuts to be exploited in this fashion.
In Bender's Big Game there is a scene where Fry is playing basketball with his brother and he still has the 7-leaf clover. Also in that version of history Bender stops by the Yancy's house looking for "Philip J Fry" and is taken to the nephew. So we know the nephew was still named for Fry, and it's possible that he was given the clover later.
So one could assume that Philip just ends up disappearing later than we were at first led to believe.
That is about the best I can do to cram to two together. Realistically, the authors are probably taking liberties in how time is going to be handled starting with Bender's Big Game and moving forward. The fact that the ex-girlfriend is now in our time instead of the future tells me they have "branched time" and the previous timeline of Futurama has been shifted.
Nothing was altered, except that Phillip Jr. knew his uncle for a little bit before Fry disappeared again. They would still miss Fry no matter when he disappeared.