Inconsistent contract estimate before and after renovation starts

[Yangyang Jin]

I acquired 4 new units in the beginning of the year, and lined up renovation work to start in July. The contractor I am using is the person I have worked for over 4 years and in general trustworthy, and willing to explain the work he is doing. I asked for a quote of rennovating all 4 units, price look good and I did not consider asked around for quotes for comparison. And I had lot of confidence of starting the renovation work with him. However, I was very shocked when he provided an updated estimate for the 1st unit he started working on, the price was 50% more than the original quote. We had the discussion, and he tried to explain, but somehow the math still does not add up. I went through the original quote and the updated quote in detail, thought they way he did the estimate was not consistent and confusing.  The categories shown in his estimate is completely different, so it's hard to compare apple to apple, and understand why the big difference in cost. There is some major structural work was not considered and known in the original estimate, which I can understand, but that is still far from the 50% bump. 

The 1st unit is at the end of the renovation work, but there are 3 units left and need to start the renovation soon. I am very eager to hear what do you think and would love to get more quotes to understand if what the contractor is charging reasonably?