The short answer to your question is yes.
The two limited companies are separate entities.
The 50% company engaged someone else or another limited company in your case to do some work and that other limited company is entitled to be paid the full amount but it would cost to do the job regardless of who did it. Any profit that you get as a result of the eventual sale or whatever it is of the property stays the same.
That answers your question.
The fact that whoever they contracted to do the work was a limited company which just happened to be owned by you is irrelevant.
There is a potential conflict between the directors duties of the 50% company and your personal interest in your wholly-owned company but that’s a different issue than you are asking about.
Can I clarify anything else for you?
I am happy to answer any specific points arising from this.
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If you still need any point clarifying, I will still reply because the thread does not close.