I'd like to remove
index.php from joomla URLs.
Though I'm little worried that this can affect keyword positions in google.
Is it safe to turn this parameter ?
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Yes it is safe - its built into the joomla core to do so. All you need to do is rename the htaccess.txt to .htaccess and then enable it in the joomla global configuration screen.
When SEF is enabled on a Joomla website, the old non-sef urls still work normally so search engines will still be able to find the pages whether they use the SEF or non-SEF url.
These days, Google isn't likely to penalise you if it finds multiple links for the same content on the same website but it might help if you install OSMap or similar and submit a sitemap to Google Search Console (formerly known as Webmaster Tools) to help Google find all the SEF links.
If the search engine rankings are adversely affected, it's likely that this would only be a short term problem until Google has recrawled the entire site and found all the new links.
If you are cautious about search engine rankings being affected, then you could install a third party extension such as sh404SEF or similar which redirects the non-SEF urls to the SEF urls and this may result in a smoother transition.
For more advice on dealing with duplicate content, see the excellent answer by @FFrewin at: https://joomla.stackexchange.com/a/5541/120