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It's not a frequent problems, but…
 When ever I update the .htaccess file through admin tools it resets the php version back to 5.2 which causes the site to go down until I log in to the server and reset it to 5.4.

Do you know why this occurs? How can it be avoided?

Your PHP version is being switched from the host's default 5.2 to the 5.4 you are using with a command in the .htaccess file, probably an AddHandler command. You need to add that line to one of the extra commands fields in .htaccess Maker. That way the line is included when you regenerate your .htaccess file.

The format of the AddHandler line varies from one host to another, so I can't tell you exactly what it should look like. You host can tell you what line you should add.