I assume their titles as Kings of Bohemia and Hungary would theoretically be higher, but it seems like the crown was very centered around Vienna and Austria (as evidenced by the Austrian title being the one retained post-HRE).
Is there any example of what title they used in-between Holy Roman Emperorships (I.e. after the death of the last emperor, but before election as King of the Romans)?
I'm also interested in what would happen if they actually lost Emperorship long-term, in terms of peerage rules at the time and similar historic precedent.
Well, I only speak for Maria Theresa, but when she fighting the War of Austrian Succession, she went by the title of Queen of Hungary. This lasted until , her husband Francis I was elected as HRE. Following the election, she used the title of Empress of the HRE. You have to keep in mind, that while Vienna was the main court of the Habsburgs, other Emperors had used cities such as Prague or Budapest as their court. It really is not until you have the reign of someone like Joseph II that the court becomes centered on Vienna.
Peter Judson, The Habsburgs: A New History Derek Beales, Joseph II: Volume 1, In the Shadow of Maria Theresa, 1741-1780
During the Habsburg imperium, King of the Romans was essentially akin to, say, the title of Prince of Wales or Asturias today; a holder of the position was customarily elected during the reign of the Emperor whose heir apparent he was.
It's further worth noting that accession to the different Habsburg lands was generally asynchronous; a particular emperor-to-be would not have simultaneously come into all of the familial possessions. What this meant in terms of styling, of course, depended on the particulars of a given Habsburg.