Historians agree on this general narrative (For example, see: Harris’ The End of Byzantium, see page 8; Necipoğlu’s Byzantium Between the Ottomans and the Latins, see page 129; Norwich’s A Short History of Byzantium, see page 356):

• In 1378, John V Palaiologos and Manuel II Palaiologos request aid from the Ottoman sultan, Murad I, to help them overthrow Andronikos IV Palaiologos.
• For helping John V and Manuel II, Murad I was to be granted, among other things, Philadelphia, the last remnant of the ailing Byzantium Empire in Anatolia.
• However, even through John V and Manuel II successfully usurped the throne from Andronikos IV, Philadelphia was not granted to the Ottoman sultan.
• In 1390, when Manuel II was campaigning alongside Murad I, they captured the city of Philadelphia and it was officially ceded to the Ottomans.

It should be noted here, that our source for this narrative is usually Laonikos Chalkokondyles, a Byzantine historian, who was born a full fifty years after these events. Naturally, it is hard to consider him a primary source on this event. And as he doesn’t really cite any previous works, it is hard to see where his information is actually coming from (Kaldellis’ The Greek Sources of Laonikos Chalkokondyles’ Histories, see page 738).
Our other somewhat contemporary, surviving accounts suffer from similar issues as well. Doukas, a Byzantine historian was born around 1400; Aşıkpaşazade, an Ottoman historian, was born in 1400; and Neşri, another Ottoman historian, was born around 1450. However, these accounts notably differ from Chalkokondyles’ in one key way: the city of Philadelphia surrender immediately in 1390, instead of being attacked and conquered.

This was rather common for the Ottomans to do and was offered to other Greek cities, such as Thessaloniki, during the Ottoman-Byzantine wars. So, while it is still possible that Philadelphia refused to surrender, this does significantly challenge the original narrative.

And, talking about completely changing the narrative, recently, some historians, such as Stephen W. Reinert, have even challenged the idea of the Byzantine emperors, John V and Manuel II, even being at Philadelphia during its fall to the Ottomans.3 This is due to Chalkokondyles’ narrative being consistently chronologically messy and possibly faulty during this period.

Additionally, the third bullet point has also been explored. It is unclear whether John V Palaiologos and Manuel II Palaiologos simply refused to hand over Philadelphia in 1379 to the Ottoman sultan as part of the treaty or if the Philadelphians refused to become a part of the Ottoman realm.