I am using the Scanner to check if a deconstruction job is finished. However, it seems that logistics robots are included when checking the remaining number of buildings. Is this intended behavior?"

Internally, buildings are filtred as "placeable non-ghost entities", so... yes, it is intended.

Use the "marked for deconstruction" counter to track buildings that need to be removed. And a ghost counter to keep track of how many need to be built.

Thank you for the answer. When replacing something with a different blueprint, it seems like I have to deconstruct the old structures first. Is there an easy way to handle this?

Are you using an old deployer?
The new one (which is called "BADchest") has an option for super-forced construction. A detailed description of all the signals can be found in the tips and tricks.

Yes. I am currently creating a working, functional example of a Recursive Blueprint on the planet that players can reference. I used the old deployer because I want to make the most stable example possible to avoid confusion among players. I think I can switch to the BADchest if its operation proves to be stable enough.

The old deployer will be marked as depricated in the future and its crafting will be removed. (But robots will be able to build it, so a legasy blueprints will work).

For a new deployer, I only plan to add commands, so that nothing should break over time...

Is there a way to completely remove the buildings of the old blueprint when replacing it? Buildings from the previous blueprint remain if they don't interfere with the construction of the new blueprint.

So far, only using filtered deconstruction.
I do not know how long it will take to implement the "reverse construction" (It will only work for a new deployer). Stay tuned for updates.