1809 - June
Vienna
With his wife announcing her pregnancy, Emperor Francis II would move to end the war. Peace feelers were sent and received in short order. In truth, the Habsburg position was not quite as terrible as the events of 1809 hinted.
1. Transylvania, though long associated with the Crown of St. Stephen since taking the region from the Turk over a century prior, remained the poorest and most backward region in the Habsburg Empire. Very little was collected in taxes, certainly not considering the costs of maintaining control. Francis was willing to cede the land under one condition: that Romania absorb the region entirely with no further Russian advancement. Vienna had little to fear from Romania and it was likely that the Russians would soon wear out their welcome among their Orthodox cousins (though Romanians were more closely related to the west, at least linguistically) and perhaps a strong Romanian would serve Austria better as a buffer than the endless friction Habsburg Transylvania caused the Kings of Wallachia and Moldavia.
2. Serbia could be viewed in the same light. Only a generation or two had passed since Serbia fell to the Habsburgs and had proven to be nothing but trouble. Wars suppressing rebellions cost many multitudes more than any tax revenue. Like Romania, Serbia had provided little taxation or manpower to the Empire. Once Austria withdrew from the region, there seemed little reason for future conflict in the Balkans. If anything, again, the Russians would soon make themselves unbearable to the Serbs, turning the Orthodox against the Czar. If, and only if, Russia attempted to gain direct control over the region would Austria intervene....and then likely with Serbia and Romanian as allies.
3. The apparent dissolution of the Holy Roman Empire was a problem more of prestige than anything else. The Holy Roman Emperor collected a few token taxes and theoretically could call upon his subjects in the Empire...but in practice this was only nominal. In truth, the Habsburg Hereditary domains were often bled white settling problems in the Empire, which cost Austria far more than it ever received back. The fact that half of Germany formed an open Protestant alliance against him while many of the remaining Catholic states (Baden and Wurttemberg, for example) happily acted in their own best interests. The title was increasingly token and largely more trouble than it was worth.
Plus, the mooted demise of the Empire would indirectly lead to opportunity for all the "Great Powers" of Germany. Large numbers of petty little Principalies, Free Cities and Ecclesiastical states were only granted independence due to the existence of the Holy Roman Empire. In short order, these little patches of territory would be fallen upon by the larger German nations.
By July of 1809, even some of the Catholic states of Germany were formally seceding from the Empire. Baden, Wurttemberg and the Palatinate were also moving in that direction. As Austria lacked the capacity to enforce its structure, the Holy Roman Empire simply dissolved overnight.
In some regions, this was orderly. The German Confederation members would agree among themselves as to who got what. Hamburg and Bremen fell to the King of Denmark/Hanover/etc and much of Thuringia (the tiny Saxon Duchies) would find themselves invaded by the new King of Saxony, Maximilian. Prussia would receive little beyond some petty overlordships of Anhalt.
Perhaps the most surprising event was that the assorted Prince-Bishoprics were granted their independence by both the Emperor and the German Confederation. The latter had promised Trier, Cologne and Mainz sovereignty if they sided with the Confederation.
The left the largest prize, Munster, to the Emperor's brother, Anton. A Catholic region largely surrounded by Protestants, there was no local Prince strong enough to hold it. An attempt by one of the Protestant states of Germany to impose its will over the large and populous Prince-Bishopric would not be received well by France. Seeing Archduke Anton, now in his twenties, granted full Sovereignty was acceptable to all.
Austria was not above taking its share.
With the blatant refusal of the Habsburg armies to move in the spring of 1809, it became blindingly obvious to all sides that the end of the war was near. Therefore neither Austria nor Russian armies in the field acted. However, the partisans were another matter. Surrounded by Habsburg territory (or adjacent) were large Bishoprics like Wurzburg, Salzburg and Passau as well as some Imperial cities like Regensburg. The populations of these regions were German (and it was axiomatic that a German was worth 10 Transylvanians or Serbs) as well as much more developed. It was likely that these regions would offset the loss of Transylvania.
Prior to the war, if given the option of trading Transylvania for these regions in full sovereignty, the Emperor would have leaped upon it.
In truth, Francis II never thought much of Serbia as it was not a historic "Habsburg Land" like Silesia had been, thus prompting Maria Theresa to fight so hard to get it back. Serbia had a been a thorn in Vienna's collective side since nominally acquiring and the Empire could no longer afford it.
Giving up Serbia for a potential dynastic union with Italy was also a win by any measure.
While the formal peace would not be declared until 1810, the war effectively ended in 1809. The suffering, however, would not as the Russians and Romanians fell upon the Hungarian and German settlements in western Transylvania and commenced a three year campaign to evict over two hundred thousand people west to Hungary and Austria/Bavaria.
The Balkans would see even more bloodshed. The Bosniaks and Muslim Albanians would be abandoned by Austria, left to their fates. The Serbians, augmented by Russian regulars, would wipe entire villages and their populations from the map. An estimated 100,000 civilians were murdered from 1808 to 1811. The old Serbian region of Kosovo, now predominantly Albanian Muslim, was leveled to the ground, virtually depopulated.
In 1810, a concerted effort to "resettle" the Balkan Muslim population was being considered by Russia.
Out of an estimated 500,000 Bosniaks and 250,000 Albanian Muslims (and some Turks still in the region), perhaps 20% were killed during the five year period of 1808 to 1813. When the Russian ships began arriving along the Adriatic to carry them away, the Czar's minions had already selected a new home for these peoples.
By 1810, Russia had turned Mesopotamia, Kurdistan and Syria into defacto clients. The latter had only occurred recently when Russian forces aided a sympathetic Syrian claimant to the throne in a recent civil war. With a resentful Ottoman to the north, a dangerous Kurdistan to the east and an ambitious Egypt to the south, the new Sultan would remain a Russian puppet for the foreseeable future.
Thus when Russian wanted a place to stick a half-million or so Bosniaks and Albanian Muslims, Syria seemed the best place. Southern Syrian regions like Jaffa, Haifa, Jerusalem, Amman and others regions were lightly population and could no doubt benefit from European presence.
However, there was a problem: the region was already settled by local Arabs (and small quantities of Jews, Christians and esoteric religions).
But that didn't matter to Russia at all and not much to the new Sultan of Syria (it was a title the man himself picked out). If he wanted Russian support, this was what would happen.
Soon the refugees from Europe would supplant the native Arabs in most prestigious professions, eventually taking over demographically and politically as well to the great resentment of the Arabs. Blood would once again stain the Holy Lands.
The Muslim influence in the Balkans, after years of bloodshed, would finally end. This would leave much of Serbia depopulated and backwards for generations for the Muslims were vital to the local economy. An estimated 1-200,000 Muslims would remain, usually by staying quiet about their faith, often converting or just feigning as much. Others would cross into Montenegro, "Christian" Albania (meanly the Catholic part which had been annexed by Austria and, in the peace, granted independence) or Greece where, while not welcome, were at least tolerated.
After the initial orgy of violence and dislocation, the remaining Muslim population would stagnate due to a steady trickle of emigration to the "Promised Land" of the east.