Every roku box can have it's own side load. Any side-loaded channels will not be affected unless you connect directly to that roku and change something. Try resetting and re-enabling dev mode on that one, and be real sure about getting the IP address correct.
If you are doing development, you might want to consider making your side-loaded channel a private channel so you don't have to worry about it. That way you can keep it forever without worrying about the side load issue, and you can use both boxes for testing your development channel, seems like a waste to have a test environment available that you aren't using just because of a side-loaded channel. I have 5 rokus on my account, and test my new channels on every one of them before I submit it. There are a LOT of differences between roku boxes, and a channel that works fine on one will often run into bugs on another firmware version that keep it from working correctly. Test on as many as you can.
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