We do not have yet two definite branches and the both Karl and Ferdinand are to blame for the failure to secure the elective crown of Hungary for Ferdinand and the loss of Vienna and the prestige of Holy Emperor Karl is wounded as Ferdinand right now is not yet King of the Romans (but will became that like OTL as the Imperial Vicar and King Elector of Bohemia Ferdinand was much more liked than his brother by the German princes who wanted him and not the Spanish Felipe as heir of Karl).Never knew the aim of the Vienna Campaign. Seeing as the Ottomans were more interested in consolidating their rule in Hungary rather than expanding into Germany, I'd say the immediate aftermath of a successful siege is a sack of the city.
Medium term, The Habsburgs have lost most of their credibility as rulers of the Holy Roman Empire and the authority of the same is severely weakened. The Spanish Habsburgs will probably become the more prominent branch, perhaps hanging their Austrian cousins out to dry and marrying outside of the family to secure their borders and hereditary holdings.
Pretty likely who Karl (and the Spanish branch) will have all the damages while Ferdinand and the Austrian branch will benefit from it (specially if Maria of Spain inherited the Burgundian lands from her father... Austria, Bohemia, Burgundy/Netherlands and the Imperial Crown are a much better package than OTL who would likely see the HRE centralized under the Habsburgs in some generations so we would have a big Germany who include Austria, Bohemia and Benelux)...
The Ottomans can not hold Vienna for too much time so the Habsburg will have it back at the latest in few years...
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