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what do these flags imply when you see them in another county's provinces? for instance, I saw france's "transparent" flag in Jutland, which is a denmark province.

The just indicates that the minor country where you saw the flag (or perhaps the one just above it as they are slightly misaligned) "likes" the nation whose flag was shown best. This can indicate that a protectorate status might be forthcoming, but the flags appear early enough that often times you'll see them change as different nations apply their diplomatic wiles.