PP Sports released a statement on Thursday night, claiming the termination was just a "strategic adjustment".
"I didn't realize at all that it was unauthorized," Alaphilippe said, "But if that's how it is, then no worries. I'll pick myself up again and we'll forget about it."
The 28-year-old is now 16th in the overall rankings, 16 seconds behind new leader Yates.
Duplantis tried to challenge Sergei Bubka's 26-year-old outdoor record of 6.14 meters, but failed to continue after one unsuccessful attempt at 6.15 meters as darkness set in.
"Our original partnership was mainly focused on the World Cup in China. We are thrilled that this has now expanded to be a more all-encompassing partnership across all FIBA competitions."
"I was looking to take the jersey on stage six anyway so I'll go in with the same tactic - try to win the stage and see what happens."
The competition in Lausanne's Place de l'Europe played host to a fascinating duel between Duplantis and two-time world champion Sam Kendricks from the United States, whose best jump was 6.02 meters.
At Rio de Janeiro's Olympic stadium, former Chelsea forward Salomon Kalou made his debut for Botafogo but could not inspire the hosts to victory over Coritiba.
Asked whether he would be willing to return to England in the future, Bale replied, "If those options arise, it is something I'd look at for sure."
Jumbo Team's Van Aert produced a powerful sprint in the slight uphill finish to win by half a wheel ahead of Cees Bol and Sam Bennett.
"We are delighted to enter this exciting new partnership with TCL, following our hugely successful collaboration over the last two years," FIBA Secretary General Andreas Zagklis said.