First of all, it’s a common problem. This kind of erratic workmanship often happens and there are ways to correct it although none will guarantee perfection as much as properly aligned coloumns. The site supervisor should have not allowed this to happen in the first place but now there’s no choice left to him.
Firstly, it is bending moment development you must be worried about more than shear. If not taken care of the eccentricity would have given rise to additional bending moments especially at the critical locations adding up to bending stresses. But, don’t panic. All building codes provide a factor of safety against these things in colomn design though I don’t know the exact number in the Phillipino code. If it’s an eccentricity of a few inches or less than 5%, then you need not worry much and trust the contractor. He must be providing crank bars in the longitudinal reinforcement after bending the bars which is the most common technique. You can see it in the image below.
It would be very costly and also time consuming to replace the entire colomn. Especially, when the floor slab has been constructed it’s nearly impossible. If the eccentricity is large enough, you should get an expert opinion from an experienced engineer by taking him to site. There are other methods apart from crank bar too.
Also, the adjustment regarding crank bars also requires additional processes like drilling, putting additional shear reinforcement which I can’t exactly tell. You must talk to the contractor or engineers regarding that.
Lastly, don’t go willy-nilly with my answer only. It’s there so you get an idea of what’s going on. I haven’t seen the site so I have only limited information. Best would be to have an engineer look at it at the site.