First make a rectangular prism at the dimensions that encloses the spheres. Create, Boolean and set it to subtract. The target is the new prism, the tools are the spheres and set Preserve Tool Bodies? to Yes. The new solid can be assigned to be Fluid.
I don't use Freeze hardly ever, so you might have to do Unfreeze since you have been using Freeze, I'm not sure. See if this works.
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