Here is an action chain that uses the same method as calibre's comments editor to transform (clean) comments. Add it to Action Chains, which will create a chain "Clean comments for selected books". Apply it by selecting some books then running the chain. If you are brave, select your entire library.
As it uses calibre's method it shouldn't change anything that calibre's editor wouldn't change. That said, make a backup of your library before using it.
This is the template it uses to do the work.
Code:
python:
def evaluate(book, context):
from qt.core import QTextEdit
from calibre.gui2.comments_editor import fix_html
e = QTextEdit()
e.setHtml(book.comments)
ans = fix_html(e.toHtml(), e.toPlainText())
return ans