This is the dictator's trap: you preempt a coup that may or may not have even been considered. The lower-tier officers get promoted, but now they can plainly see that they can be fired, jailed, or killed based on one man's paranoia. Putin can't fire any and everyone -- he needs competent people to administer agencies so that they can at least minimally function. There will come a point at which there's a critical mass, and enough people are able to anticipate his maneuvers. Putin understood that his senior henchmen could anticipate him, so he preempted them. The next crop may not have those instincts yet, but they will, and he can't get rid of everybody. The enemies list gets longer and longer.
Still, as Maduro has shown in Venezuela, if you know who your loyalists are, and if you can give certain people an extra piece of bacon once in a while, you can stay in power a long time, regardless of how badly things get ****ed up.