I have made a rooky error when sandblasted the engine block. I thought I have blocked off every hole on that block but ...

when I removed the stump I realised that not exactly.
At the rear of the crankshaft the bolt holes of the flywheel are not bottomed as I thought - ask me how I know this!
Now since I need to remove the crankshaft to get it washed I probably rather just get the whole thing done once and for all.
I wanted to keep the oem engine block since it only had low mileage but now since every bolt is out I will not compromise so I just bite the bullet and get on to it asap. Usual bearings, valve job, pistons get done with new caps and rings etc.
Can someone tell me what exactly balancing the engine means?
I have heard so many people saying so many different explanations..