Actually...
They did adress the fact that Sue was pregnant once before and the soul of that child, Val, is apparently the one Franklin moved around (first into alternate reality where she grew up and then shoved into Sues belly) and is the one being born all the while it's a very dangerous pregnancy (due to the fact it was conceived in the Negative Zone in the Byrne days). For this third pregnancy Reed was elsewhere so Johnny asked Doom to help, and he did, which gave him the right to name the child. He chose the name Valeria, after his childhood love. So both pregnancies acknoledged, Val's the same baby, still a dangerous birth, and Sue didn't pick the name.
From FF #53: (lots of bolding...) "No -- worse... This... this is the same baby... I lost once before!" "Not long ago... traveled through... shifting realities... Franklin had a wish granted... Didn't know it... Subconscious... But I touched his mind briefly... and now I know... He... He gave me a second chance... to have the ... baby I baby I lost... but he didn't understand... hos dangerous that pregnancy was... Even Reed couldn't... save us both... last time... And now... Reed... isn't here..." From FF #54: "Your child wasn't... conceived in the... Negative Zone, Crystal... Lucky you... Been through this before... Don't want the baby... to die again!
That's the story from when current baby Val was born anyway. It's possible they've ret-conned it since then, but what would be the point? They could just not mention it, seeing as it's kinda convoluted.