Val, I don't know if this is the exact same situation, but in testing some of our email campaigns I would check a box twice inadvertently, and I could receive duplicates of every email because I was technically running through the campaign twice at that time. I think that this is a similar thing here, so if someone enters the flow based on one campaign, and then they reenter the same flow based on another campaign, they should be ok. The exception to this would be if there are any flow steps that look for whether they are asset A or asset B, and that value has been overwritten by a previous action.
Is it possible to split these into separate campaigns? It seems like it would be a neater way to do things, and you can know that once a lead enters a flow then they will continue through that flow unless you remove them from the flow.
Hope that makes sense!