I was reminded of this by the chapter mentioning Jolyne's age as being 19.
She mentions in chapter 1 that she had a high fever at age 6 and even then, Jotaro "remained in the countryside [in Japan]." If she's 19 in 2011, then she'd have been 6 in 1998, possibly extending into 1999. So, the implication with all that seems to me that she came down with some undefined illness during Part 4 and Jotaro considered staying in Morioh to be more important. Maybe.
Jolyne's broken relationship with her dad is kind of a central story point but man, I bet the rest of the Joestar family would've loved her.