I was testing the plugin. In the process I noticed my cupboard had the same space as a coffin. I removed the permission and then unloaded the plugin, but it stayed that way. I assume the only way to fix this might be to recreate the cupboard.

Obviously it's tricky how to handle this. For instance, if someone has a full container with all that space used, you can't just change it back. Where would all the items go if there was no space?

I guess the main issue in this case is that with the cupboard, there's an area above the storage that tells you how many resources you need. That no longer exists so that's an issue.

Because you must replace cupboard after adding it in block-list. On reloading plugin it only increacing storages, not decreacing

Let me then kindly consider that you add the cupboard to the block list by default. It breaks built in game functionality.