Hi, thanks for trying the mod!
Any roboport (and chest) that is not on channel 0... CAN'T be selected by the deconstruction planer, which means that I have to manually delete everything.
You're correct, the deconstruction planner won't be able to select entities that aren't on channel 0. There is a workaround however, you can use the Channel Changer tool to select and reassign all entities to channel 0. Then use the deconstruction planner again, and now it should work. Still an extra step, but it avoids having to manually delete any entities.
Blueprinting and deconstruction are still a bit of a problem. There are limits to what the mod API allows when it comes to tweaking the built-in tools, which is the reason why Friend Blueprints exists in the first place. Sorry it didn't work for you...I'm still hopeful that I can find a way to make it all work better in the future.