You can compare documents with multiple flows. To prevent FrameMaker from comparing the wrong flows, make sure that each flow has a unique tag and that the flows have the same tag.
A document can contain different flows with the same name, such as separate flows named “A” on disconnected pages. In such cases, an alert message lists the duplicate flows when you try to compare the documents. FrameMaker compares flows only if each document contains one flow of the same name.