If I enter a linked battle with Hydreigon and he lowers to level 50 will his stats be his own at level 50 including the Evs or will they be Zweilous' previous stats at that level?
Hydreigon's stats will be lowered to what they would be at level 50. This means that it will keep Hydreigon's base stats (not Zwelious's) and will keep its EVs as well. So don't worry about the fact that Zwelious evolves at level 64; it will still have the stats of a Hydreigon.
Hope this helps!
Yes, it will have all of the EVs and its stats will be lowered to when it was lv 50.
Source: experience while Playing with friends