I initially wanted to make all the upgrades and power-ups persistent but then the difficulty would have to go up much faster too and it would make it even less predictable due to the random/procedural nature of the game. This could easily lead to unexpected situations where a really good player could keep on playing indefinitely or a the player would face an "unfair" difficulty.
I have some power-ups planned that have limited usage and those will probably stay between levels.
That black box is likely an unused cube mesh instance.. I though I fixed that bug a long time ago but apparently it has returned. Thanks for pointing that out.
I used to have all game files in a sub-directory but I had to change that for the Itch.io app. I'm not sure if that is needed anymore, though.
Thank you for the feedback again!