I recall it being mentioned in TOS's writer guide that Star Fleet uniforms were not laundered or anything like that. The cleaning process basically reduced them to basic components, separated out dirt and so forth, then reassenbled the uniform as new. Kind of a one-stop recycle-n-replicate deal, from the sounds of it.
Presumably (though there is no direct evidence either way), an upgraded form of this process still was used in TNG's time.
Which would also help explain why people were getting so grubby in 'Year Of Hell', if replicator usage was as restricted as it was said to be.
I would also guess that switching to the "new" uniform would have mostly involved reprogramming or updating Voyager's replicators. Given the amount of data they were getting from Star Fleet after 'Message In A Bottle', would have thought this was in one of the downloads - unless, of course, it was given a lower priority than silly stuff like tactical or scientific data.
Could have been that they simply decided to stick with the "old" uniform until Voyager returned to Federation space. Gotta figure that starships on especially long-distance / long-term missions would be allowed some leeway on such matters.