How do I make WordPress revise an .htaccess file a certain way?

If you don’t want WordPress to overwrite your changes in .htaccess file, then make sure that you write your changes outside of the WordPress comment block, that is, either before or after this:

# BEGIN WordPress
...
# END WordPress

Think of this area as WordPress’ territory. Anything within this block, will be overwritten by WordPress once it has to make any changes to .htaccess.

This is what you can do after the WordPress comment block:

# BEGIN WordPress
...
# END WordPress

<IfModule mod_rewrite.c>
# Write your rewrite rules here.
</IfModule>