The main search/replace feature was never designed to be used for hundreds of thousands of replacements, which is why it might be slow and resource-consuming if used on a vast scale.
To get better results, use Extended Replace tool (Alt+Ctrl+R), which replaces within current selection and carries out all replacements in one go. This tool runs hundreds of times faster; and creates only one big undo step instead of tons of small undos.
Note: If you wish to Replace over the entire document, select all text prior to replacing.
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