You'll be fine....
You should have really marked it as the whole rotating assembly (crank, rods, pistons, crank pulley and flywheel) will be balanced from the factory but the whole assemblie's balance will be thrown off the first time the clutch cover is replaced anyway...... But in theory, if the flywheel is just put back on and torqed back up it should be OK. You will be very unlucky if you notice any difference in the way the car drives/engine rev's.
Steve