“Gen 6:4 The Nephilim were on the earth in those days—and also afterward”
That is not necessarily a contradiction, since the Nephilim is not a term that denotes a specific lineage, but rather the type of creature. Therefore, it doesn’t say that the Nephilim who existed after the flood were in any way descended from the Nephilim who existed before the flood. Instead, they could simply have been created by the same process as the other Nephilim were created.
I understand and discussion of the Nephilim is an entirely different topic but that they are described as existing before and after the flood could mean either they somehow survived the flood, or as you pointed out they could have been recreated after the flood. Suffice it to say there are arguments supporting both views. However, if we go down this path, it's a whole new discussion.
Getting back to the topic at hand, my point is that from a scriptural standpoint, the word "all" doesn't necessarily mean "everything" in a literal standpoint.
Gen 6:17 "I am going to bring floodwaters on the earth to destroy all life under the heavens, every creature that has the breath of life in it. Everything on earth will perish".
From a strictly literal standpoint, the above verse means God intended to wipe out everything; plant, animal, insect and microorganism.
What exactly "breath of life" meant to people thousands of years was probably different from our modern understanding. My guess is it meant destructiveness on such a scale that the probability of surviving would be comparable to that of playing the lottery and losing.
Gen 7:21 "Every living thing that moved on the earth perished--birds, livestock, wild animals, all the creatures that swarm over the earth, and all mankind."
In Gen 7:21, we are told all birds, land animals and humans died but not necessarily all plants, insects, reptiles or water creatures.
Gen 7:22 Everything on dry land that had the breath of life in its nostrils died."
Verse 22 now says all birds and land based animals, land based reptiles and possibly insects died but not all amphibians, plants, or water life.
Gen 7:23 Every living thing on the face of the earth was wiped out; men and animals and the creatures that move along the ground and the birds of the air were wiped from the earth. Only Noah was left, and those with him in the ark."
Verse 23 says every living thing was wiped out but appears to qualify itself by specifying humans, birds and land based animals.
Gen 8:11 "When the dove returned to him in the evening, there in its beak was a freshly plucked olive leaf! Then Noah knew that the water had receded from the earth. "
That the dove returned with a freshly plucked olive leaf clearly means God didn't destroy all life as he said was going to do in Gen 6:17. Either God failed, or he was speaking figuratively. Which was it? My inclination is to believe he was speaking figuratively.
I think it fairly clear from Gen 7 that the destructiveness of the flood primarily targeted land based animals and non-waterfowl. Going back to Gen 6:17, if God spoke figuratively of destroying all life on the planet, why then couldn't he also have spoken figuratively in chapter 7:21-23 when saying all land animals and non-waterfowl were destroyed?
As other posters mentioned, there is also the matter of translation accuracy but that's a topic I can't address.