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Because sites with mod_rewrite enabled (SEF in Joomla) needs an .htaccess file to work.
But why have menu links broken
Check if Securitycheck Pro is configured to move files rated as "High" to quarantine (Global configuration -> File integrity -> Move to quarantine). If so, the file should be listed under "Quarantined" into the malware scanner tab. Just disable this option to avoid this situation in a future.
why/how has it been removed?