Think about the following structure:

example.com finds to public_html/index.php

example2.com finds to public_html/SUB/e2/index.php

I wish to take example.com lower for maintenance, and thought htaccess will be the most practical way. However I grew to become worried that doing this would block use of the 2nd (unrelated) site, because towards the server it's situated within the very first site.

Would an htaccess-driven block at example.com also get rid of example2.com ?

Is not there a factor like "priority" in htaccess files?

I am talking about e.g. you initially block the use of "public_html"

after which allow use of "public_html/SUB/e2" etc. ?

Must work i believe.