You can perform empirical experiments on the topics philosophy is concerned with in the same way you can perform experiments in the realm of 'pure' mathematics. I don't think there's any such distinction as philosophy/science.
But if your observations contradict your logic? Something must be wrong. It could easily be the observations, but the more you have, the less likely it is. I think, at the very limit, deduction would have to give way to induction.
Now, assuming that by "logic" I really mean reasoning without observations, I hope my point becomes more clear. My impression is that philosophers do not really go in for scientific studies and experiments; if an idea proved logically by a philosopher contradicted sufficiently good experimental evidence, for some value of "sufficiently good", I would side with the evidence.
Hopefully my thinking is clearer now. I'm working on improving my writing, so hopefully I'll be less needlessly ambiguous in the future :).