The new NYGM RUb campaign files already have the great majority of neutral ships in convoys (only) changed to the closest Allied alternatives.
I know, because I did it. Mildly tedious, but not excessively difficult ,and no ships have needed to have their flags changed. There are a few omissions, where (for example) a convoy might enter the game in September 1941 and continue being used until September 1943. Such a convoy might still contain an occasional American ships (neutral until December 1941), just to make things interesting for the player.
Stiebler.
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