I have this router rb5009 whose license (license 5) has reaches its limit, is it possible to upgrade to license 6?

Which limit, do you mean you have reached 500 simultaneous PPPoE users and need more?
Licenses do not have upgrade discounts, so you would need to buy a full price Level6 license. Distributors sometimes offer discounts: https://mikrotik.com/buy

yes i have reached 500 pppoe limit, i want to buy license 6 from mikrotik, wanted confirmation that RB5009UPr can take level 6 license.

yes, it will

Thank you.
Lastly, will I lose my current data and configurations after the upgrading to license 6?

No, applying a new license is a matter of pasting it into the terminal and rebooting the device. Configuration will not be changed.