I need to change upgrade the PHP version to at least 5.2.0 for my new magento OS Commerce installation, but would it mess up my current store which runs on 4.4.9 (PHPCart)?
The real question is, can I upgrade without harming the old cart?
All depends on the scripts you run but under normal circumstances everything should be fine if you take the migration guide into account. Also worth mentioning is that the configuration of the php installation might cause the most problems since a lot of php4 applications tend to make use of things that are either considered bad practice or deprecated in php5 (register_globals, magic quotes, ...).
Since Magento is such a wonderful and high quality product you shouldn't have any problems using that on a php5.2 server but I'd be careful anyway.
My advise would be to leave the hosting for the PHPCart system intact and set up a separate (local) dev/staging server with php5.2 to start implementing Magento. Once the implementation is complete you can forget about phpcart and move to magento without the hassle of upgrading or migrating existing applications to a new php version.