Subfolder's .htaccces security?

Not sure if there's a lag time for posts to be published, but I didn't see my post show up on the forum after the first time I submitted it. I apologize if this ends up being a duplicate post.

Anyway, I have a question about how far the security extends to subfolders when SecurityCheck Pro deletes the .htaccess file from the main directory. My website has a forum (a Simple Machines Forum) located in its own subfolder, but the forum requires log-in, and, like many other subfolders, it has its own .htaccess file. Does this make it vulnerable to attack, despite the protection applied by SecurityCheck? Or, does deleting the .htaccess file from the website's main directory create an umbrella to shield all the subfolders as well?

Hope that isn't a dumb question. I look forward to any insight you can offer. Thank you!

I was hoping that would be your answer.
I did, both, delete the .htaccess and apply the protection settings, so it seems like everything's good to go. Thanks for your help, Joe. Have an excellent week.
Cheers,
Karl