When Jefferson was elected VP under Adams in 1796, both men still respected one another and considered the other as a friend, though they had long since acknowledged their major differences on policy matters. Adams, in fact, proposed that Jefferson function as a sort of secondary President, with a big seat at the table in the Adams administration. Jefferson was inclined to agree, but was talked out of it by Madison. That goodwill was gone by 1800, sadly, thanks much more to the Federalist and Democratic-Republican partisans than to Adams and Jefferson themselves.
If Adams had been elected Vice-President, I think he would have simply gone back to Braintree and spent the next four years working on his farm.