I'm not sure if this is a known issue, but I can't seem to find it in any thread. Normally, when the blueprint deployer tries to place a blueprint over an existing machine, it changes the machine to the recipe in the blueprint, however, in the process it deletes anything in the machine's input buffer. So if the cube happens to be in the machine, you can accidently delete it from the game.

Unfortunately it seems like I can't work around this directly in Ultracube. I'm also not sure whether it's possible to avoid it even by modifying the recursive blueprints code. It uses the https://lua-api.factorio.com/latest/classes/LuaItemStack.html#build_blueprint function, which doesn't have an obvious way to avoid destroying items. Passing a player to use as the blueprint placer might work, but it's a bit of an odd hack (what player should be used)? If that does work it might need to be conditionally enabled only for ultracube.