A deck rebuild can range anywhere from a "freshening up" with new deck or rail, all the way to a full rebuild with a new frame, decking, railing, plus any add-ons. Your needs and decision should be based on not only the materials, but what the return is on your time and energy. Replacing just the railing may work for you, but if you'll want a new deck in 5-10 years anyway, you may want to consider an all new deck as well.
Decking
If you're not comfortable walking out on your deck because of the holes in the boards, you'll definitely need new deck boards, or all-new decking, if it's in the budget. If your decking is all intact but flexes in some areas, it would be wise to check the frame to see if you have some loose joists or decking fasteners.
Railing
If you're not sure about your railing condition, consider this: if you tripped and fell towards your rail, would you trust it to catch you? An unstable railing can be fixed, but it may be more work than you'd expect. Fortunately, many wood railing parts can often be replaced individually, and it's worth it as long as they can be attached properly to a solid wood backing.
Loose wood 4x4 posts can easily be replaced, depending on how they're attached. Rotten rails may be fixable, but if the connection points are so rotten that they aren't stable, you'll likely want to replace the posts and the rails. 4x4s should either be secured with bolts through them and into the frame, or mounted to the inside of the rim with blocking all around it.
Framing
You'll want to inspect your joists, beams, and posts for weak points, which are usually near the connection points. Any areas above a joist where the decking was butt-seamed together is more likely to rot, so pay close attention to those spots. The wood around the fasteners or connectors should all be solid and dry, and shouldn't crumble or allow any fasteners to pull out of it. After you've removed your decking, you may find cracks, screw holes, or even a rotten top surface that won't allow new fasteners to be securely fastened.
"Re-skins"
Since the railing and decking are what go through the most weathering and wear-and-tear on a deck, chances are that they are going to be in worse condition than your framing.
If you are inspecting your deck and find that your framing is in much better condition than the rails and flooring, there's a good chance you can reuse your existing framing and just reskin your deck.
If you feel that your railing is in good condition and only want to change out your decking, you may be able to remove your railing, replace the decking, and add your railing back on. When handling assembled railing sections and posts, make sure you're not stressing and loosening the joints, as it may weaken it. It's also important to make sure you take notes on your railing section locations, and how and where the posts are mounted. If you decide to add decking features like a border or mullion to your decking, be sure that the additional framing is not going to interfere with any of space that the posts will need to be reinstalled. This is also the best time to replace any rotten railing posts or parts, since some disassembly would be required for that.
