Turkey probably attacks Greece to reclaim its lost territories in 1939-40, while the Western powers are preoccupied with the war. Greece loses, probably as badly as Finland ultimately did; their opponent is more competent than the Soviets of 1939-40, far more motivated, and the Greeks are going to have to keep at least some of the military to guard against Bulgarian revanchism and an opportunistic land-grab by Italy.
Post-war, unless the Turks are stupid enough to join the Axis (highly unlikely), they keep their gains, because the Allies really won't care about Greek losses to a non-Axis nation. If the Turks are particularly adroit in their timing when they join the Allies, they might even be able to grab the Dodecanese from the Italians.
So, you say that between 1941 (more likely 1942) and 1945 Turkey attacks again and Greece evacuates Ionia? That's too hard my friend ITTL.
1st. Because the Greek military and the fortifications of Ionia are not easy to overrun, especially with a strong airforce. Remember also the the Greeks are now much more experienced in modern warfare than the Turks.
2bd. Because Greece does not need to keep that much army in Albania and Bulgaria. In Albania because the Italians after the armistice will definately move a large part of their army to Northern Africa and Eastern Front, and Bulgaria because Yugoslavia watches Sofia, too.
3rd. Because the British are not going to accept anyone fooling around the Straits, especially after the Soviet counterattack. Greece has proven to serve the western interests in the region, after turning down the Italian Ultimatum, which included the term of Italian troops stationing in Eastern Thrace. Also, note that unlikely 1920, now the British are fully mobilised and more keen to use force, and unlikely 1941, the British can spare some aircraft to support the Greeks, while having suppressed the Iraqi revolt, they can move to the Turkish border stirring up the Kurds, too. Remember, that with or without Greece getting directly involved in the war agains Germany, the large Greek merchant fleet contributes in the North Atlantic convoys, like IOTL.
4th. The Soviets are not going to accept troubles around the Straits, too. Firstly, they do not like Turkey that much anymore, are she proven she 's not a potential socialist "comrade" as she was in early 1920's. Secondly because in the event of Soviet support for the Turks or mere neutrality, there's a chance that the westerners controling the Straits and providing equipment to the USSR start to have some trouble with the transportations.
Hence, with no German attack on Greece, there's not Turkish aqcuisition of Ionia. On the other hand, after the war Greece surely gets the Dodecanese and probably Cyprus, provided that Greece supports Israel (the Greek Israelite community stays intact and plays its role in that), accepts large British bases on the island and accepts significant rights to the Turkish-Cypriot community.
The problem rising of the Greek and Yugoslavian neutrality has two aspects:
1. Are the additional forces available for the Axis (not having to guard the Balkans) able to make a difference in the Eastern Front?
2. If the Eastern Front goes as IOTL, does the fact the the Soviets don't engange a column in the Balkans in 1944 mean that they move faster westwards?