Does this mean that those running Weatherlink PC software will not be able to download Weatherlink.com data from stations that upload with API v2?
The upload and download API's are different and not directly connected. We're only talking about the download API here - the upload protocols have never been publicly disclosed AFAIK.
But, that said, there are two groups of upload devices - the 'traditional' ones (WLfW, WLIP and Connect) which effectively upload from a VP2 console and therefore are subject to the VP2 sensor combination rules; and the more recent types (EM and WLL) which, in their different ways, can cope with a much more varied selection of sensors and hence cannot (comprehensively at least) be accessed by software expecting only the VP2 sensor set. I suspect that data from these two groups must be handled rather differently behind the scenes at wl.com.
The newer EM+WLL uploaders never have been properly accessible by the v1 API and needed the v2 API to be created. What's now happened is that the v2 API has also been extended to the traditional upload group, which for now at least can be accessed either by the v1 or v2 routes, according to how your software is written.
Software designed to download data from wl.com like WLfW cannot cope with the v2 API for obvious reasons (ie it's JSON rather than binary and will often have too many sensors) and presumably never will in the case of WLfW. Other programs would likely need a significant rewrite.
But there will only be a problem with older software as and when parts of the v1 API start to be switched off at wl.com. I've absolutely no idea whether this might happen soon or never. Actually, just to pursue this train of thought, my money would probably be on no changes in the foreseeable future - too many people are using the traditional approach with existing software. But perhaps what's really needed is for someone to write a utility that can eg poll a local WLL unit for data and then offer it to client programs via the traditional API - a sort of super VVP perhaps or VVP2, except that it could also generate and buffer archive data?