no it won't affect anything, after you move it open your config.php file, it will be in the root directory, then change $xcart_web_dir ="/store"; to $xcart_web_dir =""; it should be around line 104.
Hope that helps
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x-cart 4.1.6
PHP 4.4.2
MySQL server 4.0.26-log
MySQL client 5.0.20
Operation system FreeBSD
Perl 5.008008
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