I have recently bought LTD AC 10E left handed. It came with a set of 10s and it is tuned half step down. Now I mostly tune standard B or C and use a higher gauge. So if I put a set of 12s on this guitar but tune it to standard C will I have to align the guitar?
Maybe you'll need to adjust, maybe not, but nothing in what you've described suggests any risk of damage to the instrument. My advice is to make the string gauge and tuning changes you want, wait a few hours, and tweak the action (via truss rod first and saddle height second) as needed. There are tons of online instructionals for how to do this.