Alpha- I've seen the same thing too, but if you exit and reload the game, the 'colored' piracy flags disappear.
I believe the routes are no longer pirated, but a bug in the game is preventing the 'colored' piracy flags from resetting to white.
It seems kind of silly to have to save and reload just to find out if the offending civilization actually is upholding their end of the 'Stop Piracy Agreement', but that is the case.
Add it to the list of bugs- err, unintended features of this software.
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