I've never seen a good reason to work with a single, huge HTML file.
As Lumpy pointed out, Calibre (and Sigil) both have search (& replace) settings that control the scope.
Spell check is one of the few tools that does NOT have that control. But since yo can double click the word in the S C, and it will jump to the next occurance, there is no 'blind faith' correcting there.
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