i now see that I may have worded my problem wrong.
I did not move the files, they are in the same place they always were, i just changed the domain name (domain name in SQL base, and base url in settings.inc.php ), but it indeed seems like some of the files are not loading, especially image files(there are none)
before the change they were located in mysite.pl/shop, now i changed the domain in sql to myshop.com, and the base url in config file to "/" to display the webiste as myshop.com. I've also configured the redirection in the domain administration.