Folder Compare Miscellaneous Settings

Session > Session Settings > Misc

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To force a different alignment

By default, a folder session aligns files and subfolders by name, left and right.  Click the New button to add an Alignment Override.

Note The easiest way to manually align two items in a folder session is to right-click the first item, pick Align With, then click the second item.

To override file format associations

The Enabled file formats list lets you override which file formats will be used by this folder session.  A file format is listed in bold if its enabled state in this session is different from its global enabled state.  You can create a custom file format that is enabled for use in this session but disabled in the global list.