It is supposed to only rewrite url's that have the index.php/<something>, I sent you a PM as well, the one I sent probably needs tweaking to:
RewriteRule ^index.php/(.+) $1 [R=301,L]
So that something must be after index.php...also this will need to be placed higher in your rules before it gets to other processing.
Sometimes it is better to have individual rules, but if you can find a single statement that applies to all of them then it's much easier to use that. The trick is finding it.

If it makes you feel better I have literally hundreds of custom rewrites in my own htaccess, Randy likes changing URL structures on me

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