Chief O'Brien wore the TNG style when he returned to the Enterprise-D in 'Emissary', as well.
Though ya gotta wonder why he would beam out from a docked ship...
As for the uniform changes...durin' TNG, the first/second season style uniforms were still in use durin' the third & fourth seasons 'til the new version became the standard for everyone.
The same may be true for the DS9 style - it was added to the uniform options and was slowly phased in as the standard over time. It would easily explain why both styles were used in GEN, and why VOY had it, while Sisko used it when he returned to Earth.