There are a few different ways to do this each with their own drawbacks:
1) You could remove the <link> by selecting all your html files in the book view, right click and select link stylesheets, then clear the checkboxes. Then run your search/replace, Then re-link the stylesheets. Unfortunately most headers include " in other locations like the doctype.
2) Run the search and replace in 2 passes. The first pass to replace the ", the second pass to replace the corrupted headers with a good one. Highlight the entire corrupted header, Push the Find&Replace button to copy the bad header, then type or paste a good header into the replace field. You may have to select the "DotAll" option.
3) Perform the Search/Replace on each individual html sheet (select "Current File") and deselect "Wrap". When you place your cursor just below the header it will replace all " until the bottom of the file. This will replace any " you have in class names though, so you would have to do a second search to replace those with the ".
4) Do a first pass to change the good " to something that is not used anywhere else in the book like:
search: "
replace: zzzxxxccc
Than do your normal search(es) to fix the ".
Then search and replace to put the original " back:
search: zzzxxxccc
replace: "
5) I'm sure some of the regex guru's have a method to ignore what's inside of the <> tag symbols, but I'm not smart enough to do that - maybe they can chime in with something.
I'd recommend #4 as being the least complicated, but choose whichever method you prefer.
Cheers,
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