TL;DR: Lightning in our world can possibly do both, so there probably wouldn't be much of a change.
Lightning is a form of static discharge caused when an excess of electrons exist in one location (e.g. the ground) and a lack of them (e.g. in the clouds). This would result in, if enough potential energy (voltage) existed in the electrons, a discharge in the form of lightning from the negative to the positive.
In the scenario you give, what we actually would have is lightning going from the negatively charged planet to the positively charged clouds! As far as I understand it, lightning going from ground-to-cloud or cloud-to-ground are both entirely possible on Earth, it just depends on how the charges are split. It's also why clouds often have lightning strikes between them (distances are shorter, potential energy required for an ark is less, hence ZAP). HOWEVER, the typical strike is in fact due to "feelers" of negative charges extending downward from the clouds. The bottom of a storm cloud is typically negatively charged, and the ground is typically positively charged below it.
To answer your question, both would be possible, thus I do not see why you couldn't have the convention between them change. If you're building a world, a little hand-waving can get around most physics things (ooo, magic), especially when science itself doesn't understand the phenomenon 100%.
Some additional reading: