Time wimey stuff, and the fact that Keystone City's "disappearance" wasn't actually as long as people think it was because it gets conflated with a couple different events that happened in the city's history.

Time travel makes everything complicated, it was made complicated on PURPOSE because it fit the schemes of the men that were carrying out the crime at the time and in relation to a couple of men who are very infamous for fucking about in the time stream: The members of the Flash dynasty.

(A picture of the Keystone city skyline, with the Keystone bridge visible connecting Keystone to Central city across the Missouri river)

Keystone City has been called (both as compliment and insult) the blue collar capital of America. The city being most famous in the era from the Civil War to after WWII where it was a major manufacturing and shipping hub along the Missouri river which served as one of the country's major arteries. It wasn't until after WWI and especially after WWII where the city started to lose population to Central City across the river which also started as a manufacturing hub but eventually transitioned into a scientific and service metropolis. Ever since then Keystone City has existed in the shadow of Central City and might have been forgotten entirely if not for its people's ruthless independent streak...

and the fact the Keystone City is the birthplace of The Fastest Man Alive.

Jay Garrick was born and raised in Keystone during its heyday and when he became the Flash the city naturally became his stomping grounds. While he did plenty of work during the war in Central he always maintained, and maintains to this day the Keystone is his home and he has a deep attachment to the city.

By that same token, many of Garricks original villains also found themselves dug into the city like ticks. Many of them going underground after the passage of the Keane Act forced the mystery men to give up the fight. While this would have made any city in the country easy pickings for the villains, many of the more theft-oriented villains no longer saw any challenge in stealing for a society that had willingly disarmed itself. Two of said villains, The Shade and The Fiddler spent many decades in retirement and it was only AFTER the appearance of the second Flash (though before the reappearance of the first) that they made their move.

Combining the Shade's power over darkness with the Fiddler's ability to induce hypnotic suggestions with his specialized fiddle they coated the city in a dome that produced a strange...cognitohazard, for lack of a better word. It made it so observing the city or commenting upon it from the outside just...slipped off of people's senses. If you were to place a camera at the edge of Central City, it STILL would have seen the giant shadowy dome encasing Keystone across the water but no one viewing the PHOTOS would have been able to notice anything out of the ordinary in them.

This status quo existed for only about four years until the first and second Flashes teamed up, defeated the duo and freed the city (the residents of the city itself were under a similar but opposite effect, basically kept from noticing that the city was cut off from the outside world). People THINK the separation was much more extreme than it actually WAS because they conflate the city's captivity with Jay Garrick's forced retirement and disappearance which happened DECADES before and left the city itself mostly untouched.

(Shoutout to @adorkastock for the pose reference, many thanks!)

Injustice

(Original and my ref from said BTBATB comic👇) >:3