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If the files contain field with the same name you will have to flatten them first, then combine them.
You can do that using the Preflight tool or an Action that executes a simple script:
this.flattenPages();
Just be aware this is NOT reversible, so make sure to save the files under a new name, or to keep a backup copy of the editable files somewhere.
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I don´t know about the Preflight tool but, from looking it up, seems complicated. Wished there was an easier way to do what I want.
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You can create a Custom Command with the code I provided. It's quite easy to set up.
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Another methodology is to extract and combine the data, since it is usually the data you're after anyway. Acrobat Pro provides a feature for doing exactly this in "Prepare Form" mode.