Our SEO team was working on a website and they had made some changes to the .htaccess file and uploaded it onto that website. The problem was that they did not know that the website already had its own .htaccess file. Hold on! Why did they not know?
That’s because the FTP client did not show the file. This does seem surprising but it’s true. FTP clients do not generally show the .htaccess file and you have to manually make some settings to the FTP client so it shows up.
So, after the file was overwritten the website URLs stopped working and we had to download the SEO module afresh and make the relevant changes and re-upload it.
The moral of the story: Don’t believe your eyes. Use a bit of your head. If the website has SEO friendly URLs enabled and its hosted Linux then there MUST be an .htaccess file there.