Same idea as Zvika, there are posting profiles for everything, so if your vendor invoice is currently set up to require a department financial dimension, you would have to adjust that. If it's not in the posting profile, the department would be defaulted from somewhere, i.e. the vendor, the procurement category, etc., so you could delete it there so it wouldn't pull the value you don't want into the vendor invoice.
If it's more an issue of "deleting" that department, you can suspend it as Zvika suggested.
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