htaccess conflicts in subdirectories?

whether having 2 htaccess files can cause a conflict

[mikewex]

I was wondering whether having 2 htaccess files could be causing a conflict with an SEF URL generation. I wonder if the .htaccess in the root to create SEF URLs via modrewrite is affecting a second .htaccess in /subdir subdirectory that runs another script and does the SEF for that script. The root one works fine. But the script in the subdir worked on install and then soon quit working properly. Is there a need to create an exception in the root file not to handle certain subdirectories? Many thanks to all.

[Caterham]

Is there a need to create an exception in the root file not to handle certain subdirectories

Usually not, because RewriteRules in /var/www/folder/.htaccess will override rewriteRules stored in /var/www/.htaccess by default.