Until 1804, Austria was not an Empire (like usually is said), but only an Archduchy, and was linked to the Kingdoms of Bohemia and Hugary; therefore the members of the Family were Archduke(ss) of Austria, Royal Prince(ss) of Hungary and Bohemia; the Head of the Family was Apostolic King of Hungary, King of Bohemia, Archduke of Austria and he was always elected Holy Roman Emperor.
In 1804, Holy Roman Emperor Franz II elevated Austria from Archduchy to Empire; since that moment, the members of the Family are Archduke(ss) and Imperial Prince(ss) of Austria, Royal Prince(ss) of Hungary and Bohemia; this is the title they still have nowadays; the Head of the Family was now Emperor of Austria, Apostolic King of Hungary, King of Bohemia and elected Holy Roman Emperor; that's why HRE Franz II became Emperor Franz I of Austria.
In 1806 the Holy Roman Empire was dissolved.
When in 1804 HRE Franz II elevated Austria to the Imperial status, he also stated that the Head of the Imperial Family bears the title of Emperor even if he doesn't reign on any country.