Even with Terok Nor, the impression I got was that the military was told by the politicians to leave the station in a move that took them by surprise and disbelief. So they left, but with the hope of returning basically the next day. Which they almost did, in "Emissary", until Kira put up a spirited resistance.
The hope of returning resulted in them only doing a half-hearted job at destroying the station. Not only would it have been a major economical loss to have to build an all-new station at the expected return, but it would have been time-consuming - and the Cardassian military knew the Federation was out there, waiting to step in, so it would be of essence to secure defensible positions ASAP after the politicians got their "withdrawal" silliness sorted out.
The military was in poor position to dictate anything at that time, of course: they had been thoroughly humiliated in "Chain of Command". It wouldn't surprise me in the least if the Detapa Council took this opportunity to force the Central Command out of all of its unprofitable and embarrassing ventures, including the already milked-dry Bajor but also Empok Nor.
It would help if we knew what Empok Nor was intended to do. It looks identical to Terok Nor, which we know was an orbital refinery with major spaces dedicated to ore processing, plus a base from which to intimidate an occupied planet. Perhaps Empok Nor was under tow, on its way to another occupied world, when the Detapa Council told the military to abandon the occupation and to pull back to defending the homeland? Abandoning the station in mid-space, still far from enemy territory, would be a safe "waiting" option; Cardassia could recover the station later on, if the need arose. It's just that Cardassian military might and conquest ambitions subsequently withered and died, leaving the station free game by the time of "Empok Nor".