The warning is designed to have you read the fine manual. The process you have to follow is dead simple. Here's what you need to know (it's in big boxes in the documentation):
If you ever want to revert to a "safe default", just set all of the options on this page to "Off" and click on "Save and create .htaccess". This will create a .htaccess file which is essentially the same as the one shipped with Joomla! (htaccess.txt).
and
Depending on your web server settings, some of these options may be incompatible with your site. In this case you will get a blank page or an Internal Server Error 500 error page when trying to access any part of your site. If this happens, you have to remove the .htaccess file from your site's root directory using an FTP application or the File Manager feature of your hosting control panel. Since Admin Tools 1.2, your old .htaccess file is saved as .htaccess.admintools. You can rename that file back to .htaccess to revert to the last known good state. If you are unsure how this works, please consult your host before trying to create a new .htaccess file using this tool
Some prepackaged server environments, like WAMPserver, do not enable Apache's mod_rewrite module by default, which will always result in an Internal Server Error upon applying the .htaccess file. In this case you are strongly suggested to enable it. On WAMPserver you can click on its tray icon, go to Apache, Modules and make sure rewrite_module is checked. On other server environments you have to edit your httpd.conf file and make sure that the LoadModule mod_rewrite line is not commented out (there is no hash sign in front of it). Once you do either of these changes, you must restart your server for the change to become effective.
We strongly suggest that you begin by setting all options to No and then enable them one by one, creating a new .htaccess file after you have enabled each one of them. If you bump into a blank or error page you will know that the last option you tried is incompatible with your host. In that case, remove the .htaccess file, set the option to No and continue with the next one. Unfortunately, there is no other way than trial and error to deduce which options may be incompatible with your server.
I believe that's clear enough, right?
Regarding support, I believe that your timezone is a bit opposite to mine. I live in GMT+2 and I'm usualy awake from 07:00 GMT to about 23:00 GMT. However, the business hours –as noted in the Support Availability block at the bottom of the page– is 08:00 to 15:00 GMT. You can use http://timeanddate.com/ to convert GMT to your local timezone.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!