I created a spreadsheet with 2 workbooks.
...
The problem is, I have an "IF" statement in J45:
if(j45=sum(J8:J9),"","Not Balanced")
Which if it equals, the cell will be blank, if it doesn't equal, the
cell will have "not balanced"

This does not work all of the time, even when the sum of J8:J9 equal
cell J44.

While I didn't follow the details of your example, I have had this kind of
problem before. Sometimes, it's a rounding problem. Maybe things would work
better if you used something like:
if(ABS(j45-sum(J8:J9))<.005,"","Not Balanced")