The BoE is independent (in theory) from the government.
If the bonds that BoE own go to zero, their entries are effectively just deleted from the database.
In the same way that an increase in the number of £ in the database doesn't increase the government's deficit.
It's a very simple concept but can have psychological hurdle to overcome, given the simplicity of it and implications once internalised.
Analogy .. BoE has root admin access to the database of £. Government does not, has read only access.