And then I slept, and upon waking, viewed the situation with fresh eyes. There is a way in which this game might affect the main series, and will affect any fans of the series that play the game. TES:O is going to take place in all of the provinces, including the ones that haven't been seen in a TES game since Arena(which I haven't played). So at the very least, the manner in which the provinces are represented will influence player expectations when said provinces are featured in future TES games, and could possibly influence how Bethesda portrays them.
Now I just want to put this out there: this does not have to be a bad thing. In Oblivion, Bethesda showed that they are quite willing to retcon their own lore by changing Cyrodiil from a jungle to a standard fantasy setting. If Bethesda holds ZeniO to the lore, it's possible that this could prevent future retcons(although the manner in which they changed Cyrodiil demonstrates that a lot can happen in 1000 years).
The biggest potential problem is that if Bethesda does decide to change the province from what appears in TES:O, some players may actually prefer the ZeniO version and find them disappointed with the original studio's vision of the province. In any case, I hope that Bethesda is at least providing some consultation to ensure that the look and feel of the setting stays in keeping with their own future plans.