If I select everything again and run another find and replace, Anki will now replace 0 (no cards).
Anki will only accept to replace another card if I select its html field and hit Ctrl+Shift+X (to view the html, as my first screenshot). Now, after seeing that card html, and I select all cards again and run another find and replace, Anki will replace only 1 note again.
After I searched and replaced with the expression <br\s*/\s*> it replaced all except one <br>.
I filtered the decks with "re:<br", and I found only one card. Then, I repeated the search and replace after seeing the html with Ctrl+Shift+X and the last card was finally replaced.
I tested this with Anki 2.1.22, 2.1.8, and 2.0.52 and the behavior was the same.
Thanks! With the latest beta, I can see my html fields are mostly <br /> instead of just <br>, now it makes sense that only <br\s*/\s*> would work to remove the <br> tags.