2C-I works by the same mechanism as other psychedelics like acid and mushrooms, and I'm not aware of any evidence that it's a serotonin releaser or uptake inhibitor or anything like that. Tripping on 2C-I shouldn't disrupt your brain's serotonin levels. Some people find psychedelics less intense for a while *after* an MDMA experience, but doing them in the other order (2CI, then MDMA) shouldn't produce any major cross-tolerance.
I've never combined these two specifically, but 2C-E and MDMA was pretty a spectacular flip. I have used 2C-I multiple times a week for a couple weeks at a time before and, while tolerance built up and made the peaks less intense, I didn't notice any long-term serotonin depletion, and I'm pretty sure I took molly at least once during that 2C binge and had a good roll.