the key to the issue is in debugger port. I was having the same problem, I was killing every process listening on port 8081 (my http port), 1099 (JMX port), tomcat shutdown port, every java.exe, and still nothing.
The thing is this debugger port is different. If you run the application, it will go through the port you have Tomcat configured for, 8080, 8081 or whatever. But if you run it in Debug mode, it goes through a different port.
If you go edit your Tomcat configuration from IntelliJ, the last tab is Startup/Connection. Here go see the configuration for Debug mode, and you’ll see its port. Mine was 50473. I changed it to 50472, and everything started working again.