Your right, taking your rifle apart can affect your zero. I only take my rifle apart after a particularly wet trip. Next time you have the rifle apart give the hidden bits a spray with WD-40, let it dry before you put it back together. I did this on my blued Rem 700. Bits that hadn't been sprayed had some surface rust, the bits I had sprayed had none. Don't spray it on the trigger area, bolt as it can gum things up after awhile.
On a few makes the scope rail bolt does enter the bolt lug area, if it is not touching the bolt you will be fine, you'll know if it is touching the bolt.
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