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Let's make sure that the problem is indeed caused by Admin Tools. In order to do so, try the following:

1. Try setting the Error Reporting level in your Global Configuration to "None". Many errors are caused by harmless PHP Notices and Warnings being output to the browser, breaking anything which requires HTTP header manipulation such as Joomla!'s session management, AJAX calls and download systems.

2. Try to replicate the issue after disabling the "System - Admin Tools" plugin. If you can still replicate the issue, it is not caused by Admin Tools. Disabling that plugin means that Admin Tools code (including the Web Application Firewall) is not running on your site.

3. If you suspect an issue with the .htaccess file, replace its contents with the contents of the stock htaccess.txt file shipped with every version of Joomla!. If you are on GoDaddy please wait for 1-30 minutes for the changes to be effective. Then, retry loading the problem page. If you can still reproduce the error, then it is not caused by .htaccess Maker.

If doing any of the above resulted in the issue still occurring, it's not related with Admin Tools and I can't help you. If doing any of the above did stop the issue from occurring, we'll have to do some troubleshooting.

First go to Admin Tools, Web Application Firewall, Configure WAF. Make sure "Log security exceptions" is set to Yes; if it's not, set it to Yes and click on Save. Now try reproducing your issue. Immediately after that, please go to Admin Tools, Web Application Firewall, Security Exceptions Log and go to the last page. The last log entry should have the date and time of when the issue occurred. Please copy the Reason and Target URL here so that I can help you.

If, however, you do not see a log entry, or the Date and/or IP address do not match your last access, this problem is not caused by Admin Tools' WAF. In this case, you will have to do some .htaccess troubleshooting. You may need to read the general .htaccess troubleshooting page, as well as the page on finding out necessary .htaccess exceptions.

That someone just screwed up your site, once and for all. Thank him for nothing. By removing all the #__assets records you have destroyed Joomla!'s ACLs. This may cause funky things to happen, like articles not appearing in the front-end unless you open and save them one by one, regular users or huests gaining access to administrative functions of components and so on. Rebuilding the assets table manually is not an option (uless you are a developer with 10-12 hours to spare). I would recommend buying ACL Manager (it's a dirt cheap 15€) and using its Diagnostic feature to fix the assets table automatically. You get to click on a button labelled "Fix Asset Issues", wait about 20 seconds and your site is back into working order.

Before you ask: yes, I've tried it on live sites (including this one, when I botched the migration of categories from the old J! 1.5 site) and no, it's not an affiliate link. I am a customer of Sander and his a customer of mine, but that's all.

I am sure that he meant no harm, but that's what you get on free public forums. There's always the possibility that someone with inadequate knowledge to be correct and enough knowledge to be harmful posts a reply. The problem is that the solution does seem to work and the new problem it introduces is not apparent. Oops :)