Should I say
If you haven't recovered the payment within 6 days, paypal will cancel it.
If you don't recover the payment within 6 days, paypal will cancel it.
I think the first one is the best because within 6 days is a period of time.
The first one would be considered to be more polite and would probably be spoken by someone working in customer service. The second is more blunt and might be spoken by someone you know personally, or even by someone that does not like you.
In English (or at least, American English) directly attributing an action to someone else can be considered overly familiar or blunt. "If you don't..." lengthens to "if you do not." The "do" verb is used to show direct action. "If you haven't..." doesn't presume to assign any action to "you," it merely talks about the circumstances that arise if you somehow happened to not recover the payment. This is a really basic example that would probably not offend anyone if you were to use the "don't" option, but the principle is the same. In particular, the "do" verb can be a strong one if you use it on someone else, because you come close to making a declaration (ordering them). Most businesses choose to avoid risking sounding rude by using more passive language.
The first one puts more emphasis on the final state after six days, and the second puts more emphasis on the action of recovering the account. Both are completely correct, though.
First one in my opinion, because i'ts not so offensive/negative: "If you don't..." makes me feel like I'm being accused. :) You might also want to consider "If payment has not been recovered within..." Just a thought.