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Then you would need to use 2 Input tools with the wildcard method that @Ladarthur mentioned, one pointing to each folder. There are a couple of ways to accomplish this, but if the schema's are indeed the exact same I think that would be the easiest.
- use the directory tool and search sub-directories, apply to filter to split to two data streams on directory A and B, then use dynamic input configured to update Full Path to Union files together.
- Use two Excel File Openers pointing one to each directory