The Ottoman Sultan Mahmut 2 died in 1839, just as the tensions were rising with Egypt. At the time the Ottoman navy was in Dardanelles, waiting for orders under the command of Fevzi Pasha. Fevzi Pasha had proven to be a paranoid man previously, and had stalled his advance during the late sultans sickness, to check if there were any rumours to replace him after the Sultans death. His men returned after Mahmuts death, with rumours. According to rumours Sultan Mahmut was poisoned by Fevzi Pasha’s rivals, Husrev and Halil Pashas. According to rumours these men plotted to kill Sultan Mahmut to increase their influence in the court. Fevzi Pashas paranoia was then reinforced by news that a number of ministers were sacked from their positions. On top of that some even more nonsensical rumours spread. Fevzi Pasha started believing that Husrev and Halil Pashas were conspiring with Russians and were preparing to surrender Constantinople to Russia. Worried that he would be sacked from his position or executed by his rivals in capital Fevzi Pasha decided to go to Egypt instead. His decision was influenced by the admiral of the French fleet in the region Lalande. Lalande recommended him to sail to Egypt and March with Muhammad Ali to liberate Constantinople from Russia if rumours were actually correct. It is also noted that the Ottoman naval officers did not want to fight Muhammad Ali at this point. One thing to note here is that Fevzi Pasha nor his officers saw defection as defecting to a foreign power. Muhammad Ali was an Ottoman Pasha and at this point he was seen more of a political faction within the Empire than a foreign ruler. Many times in Ottoman history rebel leaders were recognized as governors who acted independently just like Muhammad Ali did. For example Camboladzade, a celali rebel overrun Syria, and then had to be recognized as the governor of the region by the Sultan. So there was no reason for Fevzi Pasha to treat Muhammad Ali anything other than a political faction within the Empire.

So what happened after Fevzi Pasha went to Egypt? At first the Ottoman navy did not enter the port as Fevzi Pasha negotiated with Muhammad Ali. In fact Fevzi Pasha and Ali were also political rivals, with their rivalry against Husrev Pasha being the only uniting factor. After a while Muhammad Ali asked the Ottoman navy to enter the port, claiming that he was worried about a British attack. Ottoman sailors were given Egyptian uniforms immediately afterwards. Though Muhammad Ali informed Constantinople that he was loyal, and he had no intention of seizing the navy. The relationship between Fevzi Pasha and Muhammad Ali started detoriating shortly afterwards. Muhammad Ali did not trust him, but he also was dealing with financial problems. Egyptian treasury did not have the funds to pay for the wages of the sailors, causing further discontent. Lack of the required money for sailor wages prevented Muhammad Ali from officially seizing the navy for a while. Meanwhile messengers from Constantinople ordered Muhammad Ali to send Fevzi Pasha to the capital. Muhammad Ali responded to this by appointing Fevzi Pasha as the captain of the Egyptian navy. Meanwhile majority of the Ottoman officers were arrested or had “disappeared”. Likely deserted their posts. At the end Muhammad Ali lost the war and returned the whole navy alongside with the officers. Fevzi Pasha remained in Alexandria and died in 1842.

I can’t answer the last question well. I’m battle of Ankara against Timur, Ottoman soldiers from Anatolia defected to Timur, leading to Ottoman defeat. I would also recommend reading about Jalali revolts as troops constantly defected to rebels.

Sources:

Donmez, A. 2016. Sutad. THE FACTION CONFLICTS AT THE SUBLIME PORTE: THE CASE OF AHMED FEVZİ PASHA’S SURRENDER OF OTTOMAN NAVY TO GOVERNOR OF EGYPT

Kutluoglu, M. 2018, TDV Islam Ansiklopedisi. Kavalali Mehmed Ali Pasa