If Scotland votes Yes, there is no automatic entry into the EU but is it really conceivable that the EU would revoke the EU passports of 5.3 million people that live in an independent Scotland, revoke the rights of Scottish people who work in other EU countries from having the right to work there, revoke the rights of citizens of other EU countries (including from the rest of the UK) to work in Scotland, revoke the right of Spanish, French, Danish and other EU fishermen to fish in Scottish waters, etc etc etc etc etc etc etc.
There is no such thing as an EU passport.
Persons living in Scotland hold British Passports, French passports, Irish Passports and passports from many many countries.
EU has NO say in what occurs in Scotland regarding passports and attempts to claim as such show a deep ignorance of the split between National and EU rules.