Was able to hide "index.php" from URL in Joomla, but links don't work

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I selected "yes" for URL rewriting in global configuration (protostar). I changed "htacess.txt" to ".htacess". I was happy to see the "vanity" links -- the "index.php" was gone! But, only some links worked. Others did not. There is no rhyme or reason for which link has what outcome. They are all "article" links in the same menu. I pulled my hair for two days trying to figure it out on my own (and help from the Internets) before seeking your advice. Please, please and Thank you for your help! (Be specific if I need to add or rewrite code.) I'm at my wits' end.
Hello, Sorry for the problems with the Search Friendly URLs. I'm not sure what you have done wrong that is leading to the problem that you are seeing. We would need to have backend access in order to properly see what's happening with your installation. You may want to review the documentation on enabling SEF URLs on Apache or Joomla documentation for Search Engine Friendly URLs. You should see the appropriate code to use in the .htaccess files. There are also a lot of SEF extensions that you may want to consider to use with your Joomla install that may also help resolve this issue. I hope that helps to answer your question! If you require further assistance, please let us know! Regards, Arnel C.