I happened to buy my first Casio 5600 and saw that top left button is little shorter than other only to realise later that’s by design. But before that I opened the back case and put it back again. Screwed down the 4 nuts as securely as I can .
So I my question is do I need to be worried about my water resistance as I simply put the back case on ? Or is there something I need to do with o-rings and grease every time I open the back case ?
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As long as the gasket is in the groove in the case you should be fine. G shock gaskets are generally well lubed from the factory and since yours was new you should be fine.
If the gasket and mating surface is not damaged, the gasket is seated, and everything is tightened properly, all should be well. It can't hurt to wipe a little silicone grease (aka dielectric or bulb grease) on the seal to lubricate it.
It also makes sense to check for debris, really any that can break water resistance, such as a hair across the gasket. I would also quickly inspect the gasket for wear or pinching.