Partially fixed with 5ed78fb633b448488d7ed2c758d0bf818e0a20b5. The problem was in the hash generated for storing the debugId of new objects. They could not be deleted, or even modified, due to mismatching hash values.
Still not completely functional. If the user has two items of the same type one after another in the code, and deletes the first one, the delta object assumes that the first one has been modified and the second one is the one that has been deleted. Copying the properties/property values over seems to be still broken. The effect in the live preview is that both objects disappears, and get substituted by a mutated offspring of the former, whose property values are a mix of the two.
Right now some properties cannot be changed in an existing object (e.g. "id", which is not actually a property but it's detected as one by the delta; and there seems to be also problems with user defined properties).