I think the deeper answer to your question is that there really wasn't a major switch in the focus of the Austrian Habsburgs in that particular time period. On a cursory glance it may make sense to suppose a switch in focus. The common interpretation of the Thirty Years War is that it reduce the Holy Roman Empire to a legal fiction, making the title of 'Emperor' but a prestige position. Under that narrative, the Austrian Habsburgs switch their focus to their holdings outside the Empire, reclaiming Hungary from the Ottomans and pressing deeper into the Balkans. However, on deeper examination, this doesn't seem to be the case. Even while the Austrian Habsburgs fought the Great Turkish War that began with the famous Siege of Vienna and ended with the reconquest Hungary, they were also engaged in the Nine Years' War against Louis XIV, in an attempt to protect the imperial frontier from further French reunions. This was done mostly with troops provided by the Imperial estates, while the Emperor's own troops were deeply involved with the Balkan campaigns.

To start from the beginning, the idea that the Holy Roman Empire was--to use Voltaire's famous quote--"Neither holy, nor Roman, nor an Empire" is a bit of a misconception. While far from centralised (which was true of nearly all European states in this period) the Imperial institutions existed, and were used. The Reichstag met to vote taxes on the estates to fund war, the various imperial courts attempted to handle disputes without need to violate the Perpetual Peace, and--in general--the Empire operated relatively smoothly, despite the hiccups introduced by the confessional conflict. Similarly, while international relations scholars will talk about the Westphalian state and the general idea that the modern nation-state began with the Peace of Westphalia, the Peace did not truly break the Empire. Indeed, imperial institutions remained intact and continued to process the affairs of the Empire up to its dissolution in 1815. Thus, the position of Emperor was far from an empty title, and one the Austrian Habsburgs wanted to maintain. Furthermore, while Habsburg influence in the Empire did receive a setback due to the Thirty Years War, it was far from permanently crippled.

While Ferdinand II's attempts to promulgate the Edict of Restitution and other matters that would have likely increased Habsburg influence over the Empire as a whole had faltered, Ferdinand III's own campaigns for increased Habsburg influence were far more succesful. Ferdinand III was able to get his chosen heir selected King of the Romans with relatively minimal difficulty, and was generally quite effective at Imperial politics during this time. Throughout this period, the Austrian Habsburgs remained quite concious of their commitments to the Empire, espescially given the resurgence in French power throughout the late-17th and early-18th centuries. The need to confront the French in the west remained prominent, and Habsburg influence amongst the imperial estates was crucial to gathering the necessary resources to engage the French militarily. That the Austrian Habsburgs were able to simultaneously wage war with the French and the Ottomans, even with substantial foreign subsidies, is one of their greatest military triumphs of the period.

The map may seem to suggest that the Austrian Habsburgs switched their focus to their Hungarian holdings in this period, as it saw the defeat of the Ottomans at Vienna in 1683 and subsequent conquest of the Ottoman held portions of Hungary. However, this Austrian victory was less the result of a new focus on the region, but rather the result of prosecuting a war that had begun to swing to favor the Austrians. Importantly, the ability of the Habsburgs to prosecute the Great Turkish War was heavily reliant on their influence in the Holy Roman Empire, as Imperial troops and money were used to face the French, while the Emperor's forces (along with the rest of the Holy League) prosecuted the war against the Ottomans.

Now, onto sources. I think that any understanding of the period your curious about is going to have to consider the Thirty Years War as a major part of its backdrop. As such, I can recommend either Peter Wilson's The Thirty Years War: Europe's Tragedy, or C.V. Wedgwood's The Thirty Years War as exellent works on the piece. Wilson's work is far more recent, and engages more with the general historiogaphy and arguments made about the influence and impact of the Thirty Years War, so I'd place an emphasis on that work. Now, if you're specifically interested in the Austrian Habsburgs during this period, then I strongly recommend Michael Hochedlinger's Austria's Wars of Emergence: 1683-1797. This book is very useful for an understanding of the Habsburg fiscal-military state in this period, and does seem almost tailor made for the period in question.

I hope this has helped, and please feel free to ask any follow ups!