Each time you trust a new version of a module, a new line in the fsx.cfg will be created by FSX so, if a module gets updated and trusted often, you'll have many lines for it.
However, the additional lines don't do anything, they are there only in case you'll use one of the older version, since its line is already there, a new trust request will not repeated, since FSX already "knows" that module, because it launched it at least once. Other than that, you can have many lines, but only the one related to the currently used module is needed.
In any case, our installers will automatically clean your FSX.CFG from all our entires (current and past) in the [Trusted] section, if you reply "YES" to the questions "Do you want to remove the Addon Manager?" and "Do you want to remove the Couatl script engine?", that are made when uninstalling any of our sceneries.