I don’t think they ever had a falling out at any point (not that we can ever be sure) – Polly simply took a different direction for a while after
To Bring You My Love and
Is This Desire?, and John’s style didn’t suit it – and he wasn’t interested in it either. I might be wrong but I think he also had his first kid around that time and didn’t want to go on a year-long tour far away from his family anyway – at least that’s what I vaguely remember from some podcast. In the early 00s he was also busy with his solo work, as well as scoring and producing for other people (e.g. the Sparklehorse record, which featured Polly as well). Wasn’t the original demo for “Black Hearted Love” written/recorded around that time, too? I mean, they were clearly still in touch, despite not producing full studio albums together.
It’s also worth noting that back in the mid-90s Polly was much more prolific, and John played, co-produced and toured three full-length LPs with her in a span of only four years. That’s a lot, especially compared to 7-year-long gaps between her albums we have nowadays. I think it’s only natural he wanted to do his own thing for a while in the early 00s.
As for
Uh Huh Her,
he called it “patchy”.