Are your switches Zigbee or Zwave? The thread you originally posted in was discussing a Zigbee switch, but in your case I suppose it could be either.
If it is Zwave, there are a couple ways to use the PC Controller. When you use it in the standalone mode, you do remove the switch from SmartThings. SmartThings has stopped deleting Routines if a device gets removed; however, to be safe, create a dummy virtual to insert into the Routine alongside the switch to be removed before you remove the switch.
There is a way to make the PC Controller a secondary controller within SmartThings so that you don’t have to remove the device. I have not had much success with that method, but others use it just fine. Inovelli support has/had an article on how to use the secondary controller method.
If by chance your device is Zigbee, the the PC Controller won’t work for that. You’ll need a different hub. See this thread for discussion: