If the text is already in HTML, I use this Regex, and replace one by one:
Search:
Replace with nothing.
A faster way might be to use the above search and replace with a hyphen. Then go through your typical "hyphenation search" pass and fix any unneeded hyphens. I personally replace one by one just so I can double check with the PDF that a chunk of text is not missing (Most of my work is from PDF -> EPUB).
To clean up hyphens throughout the text, I use the Spellcheck function in Sigil (Tools - Spellcheck - Spellcheck (Alt+Q)). This will give you a list of every word in the book. I then insert a hyphen in the search box (See attached image).
Then I go look at the list of words with hyphens and remove them if needed. I do one pass with "Show All Words", then a pass with it unchecked (to show only words Sigil think is misspelled). And then maybe one more pass with "Show All Words" checked. In my case, these 2 or 3 passes usually catch almost all hyphenation errors throughout the book.