Capt., you can change and resubmit as many chapters as you want (though it can only handle ten at a time). If you have them ready, then post them all at once (Often, when you're revising, you'll want to review to earlier chapters, because it'll affect later chapters, and the later chapters might change the earlier ones too).
"Do the filenames have to be the same?" Interesting question. I had one story, where readers raised some issues with the first chapter. Because it consisted of two different 'events' at the same location, I broke it into two chapters, which forced me to resubmit the entire story to renumber all the chapters. What I didn't count on, was the new chapter was listed as a 'new addition' to an already completed story, so all my old fans reread the last chapter, expecting a continuation of the story.
Yes, you can submit them all at once, and use the same file names, but be aware an extra chapter or two can change what the readers see.
The easiest way to revise existing chapters is to revise the whole thing at once. If you only have changes to a couple chapters, then just do those (they must be sequential, so if you change ch. 1, 5, 7 and 9, then you must either repost 1-9, or submit 4 separate chapters).
And, seriously, thanks for taking the time to improve the quality of your story. Not as many people will notice the new changes, but it will improve your reputation as a 'quality' writer. Our skill and our quality are what define us as authors. You can't expect to be taken seriously if your quality sucks, and quality alone isn't worth beans (i.e. you need a decent story and it needs to be well-written). If you provide both, readers will remember, and they'll trust your next stories.